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1 | 12890863 | [
{
"id": "40d63e07-2d58-4051-9921-5b8913a82752",
"type": "title",
"text": [
"The effect of transforming growth factor beta1 gene polymorphisms in ankylosing spondylitis."
],
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[
0,
94
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},
{
"id": "96bcfe01-16bd-4c43-bf22-fb3635f02e3a",
"type": "abstract",
"text": [
"OBJECTIVES: To determine whether genetic polymorphisms in or near the transforming growth factor beta1 ( TGFB1 ) locus were associated with susceptibility to or severity of ankylosing spondylitis (AS). METHODS: Five intragenic single-nucleotide polymorphisms (SNP) and three microsatellite markers flanking the TGFB1 locus were genotyped. Seven hundred and sixty-two individuals from 184 multiplex families were genotyped for the microsatellite markers and two of the promoter SNPs. One thousand and two individuals from 212 English and 170 Finnish families with AS were genotyped for all five intragenic SNPs. A structured questionnaire was used to assess the age of symptom onset, disease duration and disease severity scores, including the BASDAI (Bath Ankylosing Spondylitis Disease Activity Index) and BASFI (Bath Ankylosing Spondylitis Functional Index). RESULTS: A weak association was noted between the rare TGFB1 +1632 T allele and AS in the Finnish population (P = 0.04) and in the combined data set (P = 0.03). No association was noted between any other SNPs or SNP haplotype and AS, even among those families with positive non-parametric linkage scores. The TGFB1 +1632 polymorphism was also associated with a younger age of symptom onset (English population, allele 2 associated with age of onset greater by 4.2 yr, P = 0.05; combined data set, allele 2 associated with age of onset greater by 3.2 yr, P = 0.02). A haplotype of coding region SNPs ( TGFB1 +869/+915+1632 alleles 2/1/2) was associated with age of symptom onset in both the English parent-case trios and the combined data set (English data set, haplotype 2/1/2 associated with age of onset greater by 4.9 yr, P = 0.03; combined data set, haplotype 2/1/2 associated with greater age of onset by 4.2 yr, P = 0.006). Weak linkage with AS susceptibility was noted and the peak LOD score was 1.3 at distance 2 cM centromeric to the TGFB1 gene. No other linkage or association was found between quantitative traits and the markers. CONCLUSION: This study suggests that the polymorphisms within the TGFB1 gene play at most a small role in AS and that other genes encoded on chromosome 19 are involved in susceptibility to the disease."
],
"offsets": [
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{
"id": "029fbfd5-d042-48b8-99f9-0f740f4dcb34",
"type": "gene",
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"transforming growth factor beta1"
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15,
47
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{
"id": "0b615d3a-de4c-4e4d-9843-86f455dc0fb3",
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"text": [
"TGFB1"
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202,
207
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{
"id": "ea85c34d-9474-40b2-983e-d0b25c031614",
"type": "gene",
"text": [
"TGFB1"
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202,
207
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{
"id": "5cc331a5-399c-4ce7-aad3-27440f6af7b5",
"type": "gene",
"text": [
"TGFB1"
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202,
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"id": "386f0b86-8664-490b-8dda-22b9ea316b46",
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"TGFB1"
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{
"id": "4bb79446-ca70-43b0-a597-aa676b7f91b9",
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"TGFB1"
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202,
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{
"id": "480f3fb7-6a69-4af2-b0ca-d84812742d4f",
"type": "gene",
"text": [
"TGFB1"
],
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202,
207
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],
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{
"id": "0cf8ea55-2aa5-46b5-98f5-8323965a4c92",
"type": "gene",
"text": [
"TGFB1"
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202,
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},
{
"id": "66836e78-5a4e-47c7-ac55-c9408ace08bc",
"type": "variant",
"text": [
"+1632 T"
],
"offsets": [
[
1024,
1031
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "1632T"
}
]
}
] | [] | [] | [] |
2 | 12915397 | [
{
"id": "3a051039-7372-4c10-aa92-e84f5a512d87",
"type": "title",
"text": [
"Uncoupling protein-2 polymorphisms in type 2 diabetes, obesity, and insulin secretion."
],
"offsets": [
[
0,
89
]
]
},
{
"id": "31219e4a-e9da-4ae0-b9be-18b6cba3dc3b",
"type": "abstract",
"text": [
"The onset of type 2 diabetes (T2DM) is preceded by obesity, insulin resistance, and impaired beta-cell function. Uncoupling protein-2 ( UCP2 ) is a widely expressed inner mitochondrial membrane protein. Common polymorphisms of the UCP2 gene have been implicated in diabetes, in obesity, and with changes in UCP2 mRNA levels. We tested the hypothesis that common UCP2 variants influence T2DM susceptibility in four parallel studies of separate populations. We typed the -866 promoter (G/A) variant, a nonsynonymous ( Ala55Val or A55V ) single-nucleotide polymorphism in exon 4, and a 45-nt insertion in the 3'-untranslated (3'UTR) region. Study populations included a case-control population study, a family-based association study, and a metabolic study of individuals who had been characterized for insulin sensitivity and secretion. To evaluate UCP2 mRNA levels, we examined a fourth population of subjects, who had undergone subcutaneous fat biopsy. All three variants showed a trend to an association with T2DM (P = 0.05 to 0.07) in the population but not the family-based association study. The 3' insertion/deletion (3'UTR I/D) variant was associated with body mass index (BMI, P = 0.035) among nondiabetic family members. Haplotype combinations were significantly associated with BMI (P = 0.028), triglyceride levels (P = 0.026), and fasting insulin (P = 0.029); highest values for the three traits were observed in individuals with the heterozygous combination GVI/AVD. In the metabolic study, all three variants were associated with an index of beta-cell compensation for insulin sensitivity (disposition index), particularly in interaction with family membership (P < 0.000001). Individuals homozygous for the -866 A allele had decreased adipose mRNA levels relative to GG homozygous individuals (P = 0.009), but the 3'UTR I/D variant had no impact on mRNA levels. We confirm modest effects of UCP2 variants on BMI and T2DM and show significant effects on insulin secretion in interaction with family-specific factors. However, the associated allele and the effects on gene expression are opposite to those reported previously."
],
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{
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"insulin"
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{
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"Uncoupling protein-2"
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[
0,
20
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{
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"UCP2"
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"UCP2"
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{
"id": "85b79b59-6d0c-47c0-8613-11f35c62abb4",
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"UCP2"
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{
"id": "c53138ed-e6d8-470d-8528-f09da052acd7",
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"UCP2"
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{
"id": "000d3fb8-ff9d-4a80-8355-499af212176c",
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"insulin"
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{
"id": "60d081b1-026d-41c0-a5a6-56ed4b8f3497",
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"UCP2"
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{
"id": "edec5133-6a45-4349-b0b3-c06c1a3b8f73",
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"insulin"
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{
"id": "5864b2fc-8e6a-4055-a28c-8bdcbb429cfc",
"type": "variant",
"text": [
"Ala55Val"
],
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616,
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],
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{
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"A55V"
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630,
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{
"id": "17b15d3a-c06a-463e-968e-d9f12134202b",
"type": "variant",
"text": [
"-866 A"
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1831,
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{
"db_name": "HGVS-like",
"db_id": "-866A"
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]
}
] | [] | [] | [] |
3 | 14523377 | [
{
"id": "c28127ba-5157-4c5d-a5bc-39df0c3f842e",
"type": "title",
"text": [
"SLC11A1 (formerly NRAMP1 ) and susceptibility to visceral leishmaniasis in The Sudan."
],
"offsets": [
[
0,
87
]
]
},
{
"id": "0c280920-0a13-4ded-b573-e2d86e681fab",
"type": "abstract",
"text": [
"Genetic susceptibility to visceral leishmaniasis (VL) is indicated by differences in incidence and clinical phenotypes between ethnic groups in Sudan. In mice, innate susceptibility to Leishmania donovani, the etiological agent of VL, is controlled by Slc11a1 (formerly Nramp1). We therefore examined polymorphisms at SLC11A1 in 59 multicase families of VL from the high-incidence Masalit tribe in Sudan. Multipoint nonparametric analysis in ALLEGRO shows a significant linkage across SLC11A1 (Zlr scores 2.38-2.55; 0.008< or =P< or =0.012; information content 0.88). The extended transmission disequilibrium test shows biased transmission of alleles at 5' polymorphisms in the promoter (P=0.0145), exon 3 (P=0.0037) and intron 4 (P=0.0049), and haplotypes formed by them (P=0.0089), but not for 3' polymorphisms at exon 15 or the 3'UTR. Stepwise logistic regression analysis using a case/pseudo-control data set derived from the 59 families was consistent with main effects contributed by the intron 4 469+14G/C polymorphism. Although the two alleles for 469+14G/C lie on haplotypes carrying different alleles for the functional promoter GTn polymorphism, the latter did not itself contribute separate main effects. Sequence analysis of 36 individuals failed to identify new putative functional polymorphisms in the coding region, intron 1, intron/exon boundaries, intron 4/exon 4a, or in the 3'UTR. One novel promoter polymorphism ( -86G/A ) was located within a putative nuclear factor kappa B binding site that could be functional. Further work will determine whether additional polymorphisms occur upstream in the promoter, which could be in linkage disequilibrium with the intron 4 polymorphism. These studies contribute to knowledge of the role of SLC11A1 in infectious disease."
],
"offsets": [
[
88,
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]
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{
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}
] | [] | [] | [] |
4 | 14635012 | [
{
"id": "187a9068-b890-46d2-972f-a29b88bb3356",
"type": "title",
"text": [
"Association of TNF-beta polymorphism with disease severity among patients infected with hepatitis C virus."
],
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0,
108
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},
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"text": [
"The pathogenesis of chronic hepatitis C virus (HCV) infection remains unclear. Tumour necrosis factor alpha ( TNF-alpha ) is alleged to contribute in the pathogenesis of chronic HCV infection. Single nucleotide polymorphism in TNF-alpha and -beta genes could influence the outcome of HCV infection. The aim was to study single nucleotide polymorphism in TNF-alpha promoter region and Nco I polymorphisms in the TNF-beta gene in patients with chronic hepatitis C. Fifty-two patients with histologically proven chronic hepatitis, who had raised ALT levels (>1.5 x ULN) and were HCV RNA positive, were studied. Genotyping of -308 promoter variant of TNF-alpha was performed by PCR with primers that incorporated an Nco I restriction site. For PCR typing of the TNF-beta Nco I restriction fragment length polymorphism, sequence specific primers were used. Polymorphism in the TNF-alpha G/G, G/A and A/A allele was not different between HCV patients and healthy controls. TNF-beta A/A allele was significantly more common (P = 0.02) in patients (28.8%) as compared to controls (12.8%), whereas no significant difference was observed for TNF-beta G/A and G/G alleles [corrected]. Nco I TNF-beta A/A was strongly associated with -308 TNF-alpha G/G (RR of HCV persistence = 4.9), indicating possible linkage between TNF-beta A/A and TNF-alpha G/G allele. Patients with severe hepatic fibrosis more frequently had the TNF-beta A/A allele as compared to patients with mild disease (P = 0.04). Immunogenetic factors, such as single nucleotide polymorphisms in TNF-beta (A/A allele), may affect the natural course of HCV infection, in particular, the disease progression. Larger studies including cytokine expression profiles are needed to fully understand the contribution of the polymorphisms described in the pathogenesis of chronic hepatitis C."
],
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{
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],
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16,
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]
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}
]
},
{
"id": "e95074d8-b071-4f87-9188-89a426ed2728",
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"-308 TNF-alpha G/G"
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{
"db_name": "HGVS-like",
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}
]
}
] | [] | [] | [] |
5 | 14645199 | [
{
"id": "2314077a-5608-42eb-9936-f5790f20b951",
"type": "title",
"text": [
"An association between variants in the IGF2 gene and Beckwith-Wiedemann syndrome: interaction between genotype and epigenotype."
],
"offsets": [
[
0,
129
]
]
},
{
"id": "80eb6127-afaa-4361-acc6-d2d308d21d6e",
"type": "abstract",
"text": [
"Beckwith-Wiedemann syndrome (BWS) is a fetal overgrowth disorder involving the deregulation of a number of genes, including IGF2 and CDKN1C , in the imprinted gene cluster on chromosome 11p15.5. In sporadic BWS cases the majority of patients have epimutations in this region. Loss of imprinting of the IGF2 gene is frequently observed in BWS, as is reduced CDKN1C expression related to loss of maternal allele-specific methylation (LOM) of the differentially methylated region KvDMR1 . The causes of epimutations are unknown, although recently an association with assisted reproductive technologies has been described. To date the only genetic mutations described in BWS are in the CDKN1C gene. In order to screen for other genetic predispositions to BWS, the conserved sequences between human and mouse differentially methylated regions (DMRs) of the IGF2 gene were analyzed for variants. Four single nucleotide polymorphisms (SNPs) were found in DMR0 ( T123C , G358A , T382G and A402G ) which occurred in three out of 16 possible haplotypes: TGTA, CATG and CAGA. DNA samples from a cohort of sporadic BWS patients and healthy controls were genotyped for the DMR0 SNPs. There was a significant increase in the frequency of the CAGA haplotype and a significant decrease in the frequency of the CATG haplotype in the patient cohort compared to controls. These associations were still significant in a BWS subgroup with KvDMR1 LOM, suggesting that the G allele at T382G SNP (CAGA haplotype) is associated with LOM at KvDMR1 . This indicates either a genetic predisposition to LOM or interactions between genotype and epigenotype that impinge on the disease phenotype."
],
"offsets": [
[
130,
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]
]
}
] | [
{
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40,
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40,
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}
]
},
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"id": "472be749-fd01-4be8-b27e-fcfe17f39ace",
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615,
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]
},
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615,
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]
},
{
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]
},
{
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],
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],
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]
},
{
"id": "bc4ddf30-6fa8-4c3d-9d28-258ac5cbaa65",
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"T382G"
],
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1115,
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}
]
},
{
"id": "d5fa00aa-4014-46a5-a8ed-cc2721ed942e",
"type": "variant",
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"A402G"
],
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1127,
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],
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}
]
},
{
"id": "f80806e4-ec68-4287-9b58-8a3ef620d554",
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"T382G"
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],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T382G"
}
]
}
] | [] | [] | [] |
6 | 14651519 | [
{
"id": "3cdb32ae-e6fc-455b-bccb-a0186971e3d2",
"type": "title",
"text": [
"Association of Fcgamma receptor IIb polymorphism with susceptibility to systemic lupus erythematosus in Chinese: a common susceptibility gene in the Asian populations."
],
"offsets": [
[
0,
169
]
]
},
{
"id": "e362e571-58c4-4740-b638-8caf2ad1de92",
"type": "abstract",
"text": [
"The association of Fcgamma receptor (FcgammaR) polymorphisms with systemic lupus erythematosus (SLE) has been demonstrated in various populations; however, the results have been inconsistent. We recently identified a single-nucleotide polymorphism encoding a non-synonymous substitution, Ile232Thr ( I232T ), of FCGR2B and its association with SLE in Japanese and in Thais. Multiple functional FcgammaR genes with polymorphisms ( FCGR2A , FCGR2B , FCGR3A , and FCGR3B ) cluster in 1q23, and some of them are in linkage disequilibrium (LD). To differentiate contributions from multiple-linked loci, comparison of different populations may provide useful information. In this study, we analyzed the above four FCGR polymorphisms of the Chinese patients and controls for the association with SLE. FCGR2A - H131R , FCGR2B - I232T , FCGR3A - F176V , and FCGR3B genotypes were determined in 167 Chinese patients with SLE and 129 healthy controls. Association was examined using case-control analysis. Allele frequencies of FCGR2B - 232T and FCGR3A - 176F were significantly increased in SLE [odds ratio (OR) = 1.67 and OR = 1.41, respectively]. Interestingly, while these alleles had a tendency of positive LD in the controls, FCGR2B - 232T was in positive association with FCGR3A - 176V in SLE, suggesting that these two alleles were associated with SLE in an independent manner. Comparison between SLE with and without nephritis indicated significant association of FCGR2B - 232T with nephritis (OR = 2.65). When the present results were combined with our previous data on the Japanese and the Thais using meta-analytic methods, highly significant and independent association was observed for FCGR2B and FCGR3A genotypes. These results strongly suggested that FCGR2B is a common susceptibility factor to SLE in the Asians."
],
"offsets": [
[
170,
2015
]
]
}
] | [
{
"id": "32f10cfe-acad-4ef1-9f84-c95b258c718f",
"type": "gene",
"text": [
"FCGR2B"
],
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484,
490
]
],
"normalized": [
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}
]
},
{
"id": "398029e1-89ea-4d3a-aa05-6e097b784388",
"type": "gene",
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"FCGR2A"
],
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603,
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],
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}
]
},
{
"id": "96d90009-93a0-40fb-ac9f-fda9b766a26b",
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"FCGR2B"
],
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484,
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],
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]
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{
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"FCGR3A"
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623,
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],
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]
},
{
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]
},
{
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],
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]
},
{
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],
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484,
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]
},
{
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623,
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]
},
{
"id": "70b809c9-77cd-49be-899d-e81401373b25",
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637,
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]
},
{
"id": "4c8a7f79-4625-4d0c-b7e2-bf9391610d83",
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"FCGR2B"
],
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484,
490
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],
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]
},
{
"id": "00eb4fda-c820-4c88-b18b-a10c7d5c9b1c",
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],
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623,
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],
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}
]
},
{
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"FCGR2B"
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484,
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],
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]
},
{
"id": "3346a6fa-feff-4972-bb17-e5af822d8715",
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],
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623,
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}
]
},
{
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484,
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],
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]
},
{
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],
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484,
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]
},
{
"id": "a6419224-709b-4fcf-bc2e-31c9315bcfeb",
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623,
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484,
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],
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}
]
},
{
"id": "1e1bc861-d13c-4e5c-bbd8-08c64d3c9b70",
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"Ile232Thr"
],
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459,
468
]
],
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}
]
},
{
"id": "e7c51062-2637-4357-a0e4-cb15f25bc632",
"type": "variant",
"text": [
"I232T"
],
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471,
476
]
],
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]
},
{
"id": "606648d1-c25a-4e7c-ad0f-f3930b45fb7c",
"type": "variant",
"text": [
"H131R"
],
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[
980,
985
]
],
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"db_name": "HGVS-like",
"db_id": "H131R"
}
]
},
{
"id": "4a89ad85-f5d3-4e2b-9981-e23654ddd082",
"type": "variant",
"text": [
"I232T"
],
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471,
476
]
],
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}
]
},
{
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"type": "variant",
"text": [
"F176V"
],
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[
1016,
1021
]
],
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"db_name": "HGVS-like",
"db_id": "F176V"
}
]
},
{
"id": "a0c35107-b2c6-49cc-aa6d-861780a7179b",
"type": "variant",
"text": [
"232T"
],
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[
462,
466
]
],
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{
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}
]
},
{
"id": "504e810e-f52a-45f1-8c76-df98cdbf49e1",
"type": "variant",
"text": [
"176F"
],
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[
1228,
1232
]
],
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{
"db_name": "HGVS-like",
"db_id": "176F"
}
]
},
{
"id": "3c8dc7e9-1369-4076-beeb-2161f3411357",
"type": "variant",
"text": [
"232T"
],
"offsets": [
[
462,
466
]
],
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{
"db_name": "dbSNP",
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}
]
},
{
"id": "dab2317a-5ab3-44c4-80cf-aa0f8f307e97",
"type": "variant",
"text": [
"176V"
],
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[
1017,
1021
]
],
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{
"db_name": "HGVS-like",
"db_id": "176V"
}
]
},
{
"id": "6cf2d546-d473-4728-84a4-2606f6f0347a",
"type": "variant",
"text": [
"232T"
],
"offsets": [
[
462,
466
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1050501"
}
]
}
] | [] | [] | [] |
7 | 14651522 | [
{
"id": "ab030e7f-dd9b-4c5f-b96e-dd62841db9eb",
"type": "title",
"text": [
"Chemokine gene polymorphisms associate with gender in patients with uveitis."
],
"offsets": [
[
0,
76
]
]
},
{
"id": "7f73221f-8077-4845-97e3-24d5c931233a",
"type": "abstract",
"text": [
"Uveitis is an inflammatory condition of ocular tissue characterized by leukocyte infiltration, tissue damage, and decreased visual acuity. Chemokines have been implicated in the pathogenesis of uveitis. Polymorphisms in the genes encoding chemokines have been described as affecting chemokine production or function. We analyzed the frequency of single-nucleotide polymorphisms (SNPs) in genes encoding CCL2 (-2518 and -2076) and CCL5 (-403 and -28) in patients with Behcet's disease (BD), a systemic form of uveitis, and patients with retinal vasculitis (RV), an organ-specific form of disease. We report that there was no association between any SNP and disease. However, when segregated on the basis of gender the CCR5 -403 AA genotype was only found in male patients with BD. Similarly, CCL2 genotypes 1/2 were predominant in males, while genotype 4 was significantly associated with disease in female patients with BD. Differences in disease symptoms and severity between males and females have been described in BD and gender-specific genetic differences in chemokine gene function may be involved."
],
"offsets": [
[
77,
1189
]
]
}
] | [
{
"id": "e8cf7785-9f1f-44c2-ac67-7c28dc272811",
"type": "gene",
"text": [
"CCL2"
],
"offsets": [
[
481,
485
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6347"
}
]
},
{
"id": "d6e889aa-63c1-45f0-92ca-fb47624bb826",
"type": "gene",
"text": [
"CCL5"
],
"offsets": [
[
510,
514
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6352"
}
]
},
{
"id": "d83d92bf-35ea-4625-9bd4-7386e89d50e7",
"type": "gene",
"text": [
"CCL2"
],
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481,
485
]
],
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"db_id": "6347"
}
]
},
{
"id": "66077cbb-d4ba-436f-8ae3-6534b9cff762",
"type": "variant",
"text": [
"-403 AA"
],
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[
804,
811
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-403A"
}
]
}
] | [] | [] | [] |
8 | 14673707 | [
{
"id": "96a2db98-c2e8-477f-885b-4c0167b4d1a1",
"type": "title",
"text": [
"Identification of a novel splice site mutation of CLCN5 gene and characterization of a new alternative 5' UTR end of ClC-5 mRNA in human renal tissue and leukocytes."
],
"offsets": [
[
0,
167
]
]
},
{
"id": "6da56781-9482-4b85-9489-b4ad49010811",
"type": "abstract",
"text": [
"Mutations in the CLCN5 gene have been detected in Dent's disease and its phenotypic variants (X-linked recessive nephrolithiasis, X-linked recessive hypophosphatemic rickets, and idiopathic low-molecular-weight proteinuria of Japanese children). Dent's disease is a tubular disorder characterized by low-molecular-weight proteinuria, and nephrolithiasis associated with nephrocalcinosis and hypercalciuria. ClC-5 is the first chloride channel for which a definitive role in the trafficking and acidification-dependent recycling of apical membrane proteins has been established. In the course of CLCN5 SSCP analysis in patients with hypercalciuric nephrolithiasis, we detected a novel mutation at intron 2 of the CLCN5 gene, a T-to-G substitution, located 17 bp upstream of the AG acceptor site CLCN5 gene, a T-to-G substitution, located 17 bp upstream of the AG acceptor site. To determine the effect of IVS2-17 T>G mutation on the correct splicing of intron 2, we studied ClC-5 transcripts in a patient's peripheral blood leukocytes by means of quantitative comparative RT/PCR, and found a new ClC-5 5' UTR isoform characterized by the untranslated exon 1b and by retention of intron 1b. This new isoform--isoform B1--was not correlated with mutation since it was detected also in control leukocytes and in renal tissues of kidney donors, thus confirming its physiological role. By RACE analysis we determined the putative transcriptional start site which is located at intron 1a, 251 nt upstream of the first nucleotide of the untranslated exon 1b. ORF analysis revealed that intron 1b retention in isoform B1 stabilizes the initiation of translation to the AGT at position 297 of the ClC-5 cDNA coding region."
],
"offsets": [
[
168,
1888
]
]
}
] | [
{
"id": "e14a1beb-2830-493e-8aa5-f5c054549049",
"type": "gene",
"text": [
"CLCN5"
],
"offsets": [
[
51,
56
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1184"
}
]
},
{
"id": "9685d880-6b9b-4a51-ad80-ba14d20d6be7",
"type": "gene",
"text": [
"CLCN5"
],
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[
51,
56
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1184"
}
]
},
{
"id": "2370722e-6a9d-4cdf-8c14-5c558c8b6c9e",
"type": "gene",
"text": [
"CLCN5"
],
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[
51,
56
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1184"
}
]
},
{
"id": "b627f1a3-1b7b-4eb4-a157-e0641438c496",
"type": "variant",
"text": [
"mutation at intron 2 of the CLCN5 gene, a T-to-G substitution, located 17 bp upstream of the AG acceptor site"
],
"offsets": [
[
857,
966
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "7053fb89-0970-472d-af77-4ffda6df62b7",
"type": "variant",
"text": [
"IVS2-17 T>G"
],
"offsets": [
[
1079,
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]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "TIVS2-17G"
}
]
}
] | [] | [] | [] |
9 | 14681301 | [
{
"id": "07a0d4ae-5a6f-4899-9672-43fa38f05bad",
"type": "title",
"text": [
"Association of tumor necrosis factor polymorphisms with asthma and serum total IgE ."
],
"offsets": [
[
0,
85
]
]
},
{
"id": "81e6a7ca-06e1-4c0a-b247-72e845628d7c",
"type": "abstract",
"text": [
"Tumor necrosis factors (TNF; TNFA and TNFB ) are major pro-inflammatory cytokines that are thought to be important in the pathogenesis of asthma. However, the functions of genetic polymorphisms in these cytokines have not been thoroughly examined in the context of asthma pathology. In an effort to discover polymorphism(s) in genes whose variant(s) have been implicated in asthma phenotypes, we examined the genetic effects of TNF ( TNFA and TNFB ) polymorphisms on asthma and total serum IgE level. Seven common single-nucleotide polymorphisms (SNP) in TNF genes were genotyped in a Korean asthma cohort (asthmatics n=550, normal controls n=171). Six common haplotypes could be constructed in the TNF gene cluster due to very strong LD between TNFA and TNFB , located 13 kb apart on chromosome 6p21. One SNP ( TNFA -308G>A) showed a significant association with the risk of asthma (P=0.0004). The frequency of TNFA -308A allele-containing genotype in asthmatics (9.8%) was much lower than that in normal controls (22.9%). The protective effects of this polymorphism on asthma were also evident in separated subgroups by atopic status (P=0.05 in non-atopic subjects and P=0.003 in atopic subjects). The most common haplotype of the TNF gene (TNF-ht1[GGTCCGG]) was associated with total serum IgE (immunoglobulin E) levels in asthma patients, especially in non-atopic patients (P=0.004). Genetic variants of TNF might be involved in development of asthma and total serum IgE level in bronchial asthma patients. The results of this study could be helpful to understand the function of important TNF genes in asthma and IgE production."
],
"offsets": [
[
86,
1736
]
]
}
] | [
{
"id": "05ece9b8-0adf-4710-b358-257cdc3dfc9d",
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"text": [
"TNFA"
],
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116,
120
]
],
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"db_id": "7124"
}
]
},
{
"id": "a74ae90f-cb87-48e0-9326-3ae2bf8376c1",
"type": "gene",
"text": [
"TNFB"
],
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127,
131
]
],
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}
]
},
{
"id": "e1c16c8a-089b-4272-ae44-eebbc8d77e58",
"type": "gene",
"text": [
"TNFA"
],
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[
116,
120
]
],
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"db_id": "7124"
}
]
},
{
"id": "a4afe27c-4eb8-4527-a340-930cf5ade96a",
"type": "gene",
"text": [
"TNFB"
],
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[
127,
131
]
],
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{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "c39497fe-1b56-43b5-9417-51863f761abb",
"type": "gene",
"text": [
"IgE"
],
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[
80,
83
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "0c7dd5dc-40a4-4d37-ab99-94986546c03f",
"type": "gene",
"text": [
"TNFA"
],
"offsets": [
[
116,
120
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "c37eb549-715e-4da2-b17c-37d56315eeeb",
"type": "gene",
"text": [
"TNFB"
],
"offsets": [
[
127,
131
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "8dc74eb3-466b-4f9d-83ab-7cdc62b2d628",
"type": "gene",
"text": [
"TNFA"
],
"offsets": [
[
116,
120
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "692882c3-ae53-4075-bf87-76f7c8d4d750",
"type": "gene",
"text": [
"TNFA"
],
"offsets": [
[
116,
120
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "acdd4537-6ce0-4a85-8ba2-f1088e493996",
"type": "gene",
"text": [
"IgE"
],
"offsets": [
[
80,
83
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "5dfc55ac-1f32-4207-8826-8fe3044aa959",
"type": "gene",
"text": [
"IgE"
],
"offsets": [
[
80,
83
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
},
{
"id": "0c2ce636-2345-4377-b0e8-a25267d81b0a",
"type": "gene",
"text": [
"IgE"
],
"offsets": [
[
80,
83
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "No"
}
]
}
] | [] | [] | [] |
10 | 14685824 | [
{
"id": "fd852a0f-0271-4b09-bbd5-68193cfd245a",
"type": "title",
"text": [
"Association between polymorphism of the dopamine transporter gene and early smoking onset: an interaction risk on nicotine dependence."
],
"offsets": [
[
0,
136
]
]
},
{
"id": "2332937c-dbe1-48d9-857c-e51928add904",
"type": "abstract",
"text": [
"Previous studies suggested that a polymorphism in the dopamine transporter gene (SLC6A3) is associated with nicotine dependence and age of smoking onset, but the conclusion was controversial. To detect the association of a G-->A polymorphism (NCBI dbSNP cluster ID: rs27072 ) in 3'-untranslated region of the SLC6A3 with nicotine dependence and early smoking onset, we recruited 253 sibships including 668 nicotine-dependent siblings from a rural district of China. The sibship disequilibrium tests (SDT) showed that the rs27072-A allele is significantly associated with smoking onset < or =18 years (kappa2=9.78, p=0.003 in severely nicotine-dependent smokers, and kappa2=4.24, p=0.058 in total smokers), but not significantly associated with severe nicotine dependence. Conditional logistic regression showed that the risk of early smoking onset by the rs27072-A allele was almost three times greater in severely nicotine-dependent smokers [Odds ratio (OR)=11.3, 95% confidence interval (CI)=1.5-85.6] than that in total smokers. Linear regression showed that rs27072-A allele also increased the risk of nicotine dependence by early smoking onset compared with homozygous rs27072-G genotype . Although these findings are preliminary and need validation, the results suggest that a polymorphism in the SLC6A3 may play important roles in smoking onset, and there may be an interactive effect between the SLC6A3 and early smoking onset on modulating the susceptibility of nicotine dependence."
],
"offsets": [
[
137,
1638
]
]
}
] | [
{
"id": "b63fdbf6-f807-4d99-8fd9-f5d6918869e2",
"type": "gene",
"text": [
"dopamine transporter gene (SLC6A3)"
],
"offsets": [
[
192,
226
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6531"
}
]
},
{
"id": "714da62b-dcf9-4f77-92f3-912be578dcb3",
"type": "variant",
"text": [
"rs27072"
],
"offsets": [
[
406,
413
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
},
{
"id": "52922527-0540-4c63-92fb-f22b441ec34d",
"type": "variant",
"text": [
"rs27072-A allele"
],
"offsets": [
[
662,
678
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
},
{
"id": "0b24e91a-35bf-42e6-b907-19ea13c40e8d",
"type": "variant",
"text": [
"rs27072-A allele"
],
"offsets": [
[
662,
678
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
},
{
"id": "053541e2-54ca-4c58-98e6-fb7ae40b97e7",
"type": "variant",
"text": [
"rs27072-A allele"
],
"offsets": [
[
662,
678
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
},
{
"id": "453a6505-d1f6-4789-b069-095744e151d3",
"type": "variant",
"text": [
"rs27072-G genotype"
],
"offsets": [
[
1321,
1339
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "27072"
}
]
}
] | [] | [] | [] |
11 | 14693717 | [
{
"id": "09fd2ddb-dc6e-4d36-a556-29d98df9e758",
"type": "title",
"text": [
"Genetic variation at the adiponectin locus and risk of type 2 diabetes in women."
],
"offsets": [
[
0,
82
]
]
},
{
"id": "2a00d122-8888-46cf-ac9a-fa49e4f10220",
"type": "abstract",
"text": [
"Previous data suggesting that polymorphisms in the adiponectin gene were associated with insulin resistance or type 2 diabetes have been inconsistent. We assessed the relationship between five common haplotype-tagging single nucleotide polymorphisms (SNPs) in the adiponectin gene ( -11365C>G , -4034A>C , -3964A>G , +45T>G , and +276G>T ), haplotypes defined by these SNPs, and the risk of type 2 diabetes by conducting a nested case-control study of 642 incident cases of type 2 diabetes and 995 matching control subjects in the Nurses' Health Study. Overall, we did not observe significant differences in genotype or allele frequencies for the five SNPs between the case and control subjects. After adjustment for diabetes risk factors, the -4034 C/C genotype was associated with a reduced risk of diabetes (odds ratio [OR] compared with the A/A genotype = 0.70, 95% CI 0.50-0.99, P = 0.04). In subgroup analyses, the +276 genotype was significantly associated with diabetes risk only among subjects with peroxisome proliferator-activated receptor-gamma ( PPAR gamma ) variant 12Ala allele (OR comparing +276 T alleles with the G/G genotype = 1.69, 1.04-2.75, P = 0.035) or among obese subjects (1.46, 1.03-2.08, P = 0.03). These data suggest a potential interaction between the adiponectin genotype and PPAR gamma genotype or obesity, but these analyses should be considered exploratory and require further investigation in larger studies."
],
"offsets": [
[
83,
1546
]
]
}
] | [
{
"id": "a419c5ac-86d9-418b-8fe7-c2a57a872977",
"type": "gene",
"text": [
"adiponectin"
],
"offsets": [
[
26,
37
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9370"
}
]
},
{
"id": "c3872780-db39-400b-836e-4554f04e7387",
"type": "gene",
"text": [
"adiponectin"
],
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[
26,
37
]
],
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{
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}
]
},
{
"id": "f37ce786-84f3-4e2b-90ed-5eac3a366e75",
"type": "gene",
"text": [
"peroxisome proliferator-activated receptor-gamma"
],
"offsets": [
[
1102,
1150
]
],
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"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "052eb8c2-8094-472e-a065-58b3b67bba5c",
"type": "gene",
"text": [
"PPAR gamma"
],
"offsets": [
[
1154,
1164
]
],
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{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "360b1d04-4738-4692-9fe8-59a0eb26d28a",
"type": "gene",
"text": [
"adiponectin"
],
"offsets": [
[
26,
37
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9370"
}
]
},
{
"id": "cf7d614f-6f54-4512-b51b-c6d8837b42a7",
"type": "gene",
"text": [
"PPAR gamma"
],
"offsets": [
[
1154,
1164
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "8ef28d03-4847-4ba4-9aea-4378b112aa7b",
"type": "variant",
"text": [
"-11365C>G"
],
"offsets": [
[
370,
379
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-11365G"
}
]
},
{
"id": "2de9b7f0-faef-4cc8-b846-b731923a6376",
"type": "variant",
"text": [
"-4034A>C"
],
"offsets": [
[
383,
391
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-4034C"
}
]
},
{
"id": "4cb5d8b6-86bb-45c7-9292-d43d34d96601",
"type": "variant",
"text": [
"-3964A>G"
],
"offsets": [
[
395,
403
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-3964G"
}
]
},
{
"id": "34ba68af-2c4e-4f2d-8434-87290db897c5",
"type": "variant",
"text": [
"+45T>G"
],
"offsets": [
[
407,
413
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2241766"
}
]
},
{
"id": "f74c53ff-def3-4392-930c-08f59ba583f7",
"type": "variant",
"text": [
"+276G>T"
],
"offsets": [
[
421,
428
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G276T"
}
]
},
{
"id": "6ab29530-d680-493d-b25b-72f7caab6318",
"type": "variant",
"text": [
"-4034 C/C"
],
"offsets": [
[
836,
845
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-4034C"
}
]
},
{
"id": "7c0b06b0-561f-49d5-ab7f-b459662e42ee",
"type": "variant",
"text": [
"12Ala"
],
"offsets": [
[
1176,
1181
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "2866402c-202e-46d1-9798-6aea7f8d5e3f",
"type": "variant",
"text": [
"+276 T"
],
"offsets": [
[
1205,
1211
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "276T"
}
]
}
] | [] | [] | [] |
12 | 14693721 | [
{
"id": "bd2e2374-17f5-4d81-ad41-605a3bf5b40f",
"type": "title",
"text": [
"The common -866 G/A polymorphism in the promoter of uncoupling protein 2 is associated with increased carbohydrate and decreased lipid oxidation in juvenile obesity."
],
"offsets": [
[
0,
169
]
]
},
{
"id": "d5e2cd2e-3206-4f3d-a024-44f9727ab258",
"type": "abstract",
"text": [
"Uncoupling protein (UCP) 2 is a member of the mitochondrial transporter superfamily that uncouples proton entry in the mitochondrial matrix from ATP synthesis. Although its physiological role remains to be established, UCP2 is considered a candidate gene for association with energy metabolism and obesity. A common promoter polymorphism, -866 G/A , has been associated with increased UCP2 gene expression and middle-aged adult obesity. In fact, our analysis of 296 juvenile obese and 568 nonobese control subjects revealed no difference in the prevalence of this polymorphism. Insulin and glucose response to oral glucose was comparable across the -866 genotypes. Metabolic studies in 147 of these juvenile obese subjects showed that homozygosity for the UCP2 promoter variant A was associated with important changes in energy metabolism compared with other genotypes, i.e., a 34% increase of carbohydrate oxidation (94 +/- 10 vs. 70 +/- 3 mg.min(-1).m(-2), P = 0.004) and a 23% decrease of lipid oxidation (26 +/- 3 vs. 34 +/- 1 mg.min(-1).m(-2), P = 0.03). Therefore, the juvenile obese subjects who are homozygous for the A variant have an increased ratio (3.6 +/- 1.2) of calories derived from carbohydrates to those from lipids compared with G/A or G/G obese children (1.4 +/- 0.2, P = 0.003), suggesting a role for UCP2 in the partitioning of metabolic fuels."
],
"offsets": [
[
170,
1546
]
]
}
] | [
{
"id": "be636ffb-0201-498d-8123-cffbb60b33a2",
"type": "gene",
"text": [
"Uncoupling protein (UCP) 2"
],
"offsets": [
[
170,
196
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "1f05c52b-325b-4743-864a-40e8ad8e0b8e",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
391,
395
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "02df7df2-012b-4f31-855a-949b98872c1f",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
391,
395
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "3575e95d-efd7-4e84-bc79-56e7cdc35500",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
391,
395
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "47ca26b2-4a59-48d6-b50d-bef399dd18ab",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
391,
395
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "a6fde834-dca4-4de3-926c-0af029390981",
"type": "variant",
"text": [
"-866 G/A"
],
"offsets": [
[
12,
20
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
}
] | [] | [] | [] |
13 | 14705223 | [
{
"id": "7a73a42d-0089-4440-9a4b-6d088a85e53f",
"type": "title",
"text": [
"Interleukin 1alpha single-nucleotide polymorphism associated with systemic sclerosis."
],
"offsets": [
[
0,
86
]
]
},
{
"id": "03e3cd17-15a1-4d9f-a85e-858dbbcc6392",
"type": "abstract",
"text": [
"OBJECTIVE: In systemic sclerosis (SSc), constitutive expression of the proinflammatory and fibrogenic cytokine interleukin 1alpha ( IL-1alpha ) by dermal fibroblasts from the affected skin has been observed. We investigated the association of a single-nucleotide polymorphism at position -889 in the IL-1alpha gene in patients with SSc. METHODS: Genotyping of IL-1alpha -889 polymorphism was performed in 46 patients with SSc and in 150 healthy controls by polymerase chain reaction with sequence-specific primers. All subjects were unrelated Slovak Caucasians. RESULTS: In SSc patients, carriers of the IL-1alpha-889 T allele were significantly overrepresented in comparison with controls (63.0% vs 42.0%; p = 0.01, OR 2.3, 95% CI 1.2-4.6). The frequency of the IL-1alpha-889 T allele was increased in SSc patients (38.0%) in comparison with controls (25.7%; p = 0.02). CONCLUSION: The IL-1alpha -889 polymorphism, previously shown to predispose to increased IL-1 protein expression, may be involved in susceptibility to SSc."
],
"offsets": [
[
87,
1121
]
]
}
] | [
{
"id": "162ec1ee-2c02-4bcb-b7c8-d74a110ae59d",
"type": "gene",
"text": [
"IL-1alpha"
],
"offsets": [
[
219,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3552"
}
]
},
{
"id": "2c1250fe-8532-490f-b444-90d9af46546f",
"type": "gene",
"text": [
"IL-1alpha"
],
"offsets": [
[
219,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3552"
}
]
},
{
"id": "6e756ab9-c442-4b10-ab8c-4bf22f4783e5",
"type": "gene",
"text": [
"IL-1alpha"
],
"offsets": [
[
219,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3552"
}
]
},
{
"id": "839c3b34-7560-4f93-89d4-1647a389003f",
"type": "gene",
"text": [
"IL-1alpha"
],
"offsets": [
[
219,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3552"
}
]
},
{
"id": "60235c79-0579-4cd1-8c43-b3332cf9aa05",
"type": "variant",
"text": [
"IL-1alpha-889 T allele"
],
"offsets": [
[
695,
717
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "53993899-173c-487e-b2ed-85e1b2c699e1",
"type": "variant",
"text": [
"IL-1alpha-889 T allele"
],
"offsets": [
[
695,
717
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
}
] | [] | [] | [] |
14 | 14709372 | [
{
"id": "05ebaeb2-d7fa-49e1-b792-d68191691237",
"type": "title",
"text": [
"Association of gene polymorphisms with coronary artery disease in individuals with or without nonfamilial hypercholesterolemia."
],
"offsets": [
[
0,
127
]
]
},
{
"id": "150c9e68-dd3e-4020-9da7-4beeac0d2dd6",
"type": "abstract",
"text": [
"A substantial proportion of individuals with coronary artery disease (CAD) has concomitant hypercholesterolemia. A large-scale association study was performed to identify separately genes that confer susceptibility to CAD in the absence or presence of nonfamilial hypercholesterolemia. The study population comprised 5248 unrelated Japanese individuals, including 3085 subjects with CAD (2350 men, 735 women) and 2163 controls (1329 men, 834 women). Among all study subjects, 2541 individuals (1688 men, 853 women) had nonfamilial hypercholesterolemia, and 2707 individuals (1991 men, 716 women) did not have this condition. The genotypes for 33 polymorphisms of 27 candidate genes were determined with a fluorescence- or colorimetry-based allele-specific DNA primer-probe assay system. Multivariate logistic regression analysis with adjustment for age, body mass index, and the prevalence of smoking, hypertension, diabetes mellitus, and hyperuricemia revealed that three polymorphisms [ 994G --> T ( Val279Phe ) in the platelet-activating factor acetylhydrolase gene, 242C --> T ( His72Tyr ) in the NADH/NADPH oxidase p22 phox gene, and 1100C --> T in the apolipoprotein C-III gene] were significantly associated with CAD in men with hypercholesterolemia. Genotyping of these three polymorphisms may prove informative for prediction of the genetic risk for CAD in men with nonfamilial hypercholesterolemia."
],
"offsets": [
[
128,
1545
]
]
}
] | [
{
"id": "2b6452b7-1a03-422a-b95c-ceb37f63ec8c",
"type": "gene",
"text": [
"platelet-activating factor acetylhydrolase"
],
"offsets": [
[
1151,
1193
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7941"
}
]
},
{
"id": "2b6acec9-a49d-4063-9b92-fa004490f800",
"type": "gene",
"text": [
"NADH/NADPH oxidase p22 phox"
],
"offsets": [
[
1235,
1262
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1535"
}
]
},
{
"id": "e2980509-872d-4fcb-81af-b1438900c77f",
"type": "gene",
"text": [
"apolipoprotein C-III"
],
"offsets": [
[
1294,
1314
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "345"
}
]
},
{
"id": "fc6a4fda-ff92-41bb-87d9-7266f13c4a16",
"type": "variant",
"text": [
"994G --> T"
],
"offsets": [
[
1117,
1127
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G994T"
}
]
},
{
"id": "ebd62163-63c7-4f34-a0d5-d3fa2da4a88c",
"type": "variant",
"text": [
"Val279Phe"
],
"offsets": [
[
1131,
1140
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "V279F"
}
]
},
{
"id": "92b2e09a-5565-41df-83b6-313003607f79",
"type": "variant",
"text": [
"242C --> T"
],
"offsets": [
[
1202,
1212
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "4673"
}
]
},
{
"id": "a71ab211-4e47-4a25-bb07-3dfec38ee9ae",
"type": "variant",
"text": [
"His72Tyr"
],
"offsets": [
[
1216,
1224
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "4673"
}
]
}
] | [] | [] | [] |
15 | 14712309 | [
{
"id": "5719c533-8dcb-4f32-aa98-b8e3139997eb",
"type": "title",
"text": [
"Polymorphisms in the interleukin-20 gene: relationships to plaque-type psoriasis."
],
"offsets": [
[
0,
83
]
]
},
{
"id": "89ddb893-cb6a-45dc-8861-ef44755d3bf0",
"type": "abstract",
"text": [
"We analyzed the frequency of single-nucleotide polymorphisms (SNPs) at positions -1053 ( rs 2981572 ), 1380 ( rs 2981573 ), 1462 ( rs 2232360 ), and 3978 ( rs 1518108 ) of the human interleukin-20 ( IL-20 ) gene by tetraprimer ARMS-PCR method. A significant association between patients with psoriasis and the G allele at position -1053 (P<0.05) was established. The pairwise linkage disequilibrium (LD) matrix showed that the nearly complete LD was present within the polymorphisms at positions -1053, 1380, and 1462 of the IL-20 gene. We found that patients with plaque psoriasis had a higher frequency of the HT3 GAA haplotype (P<0.01, OR 2.341, 95% CI: 1.346-4.074) compared to the control group. Likewise, the HT3 GAA haplotype was associated with an increased risk of early-onset psoriasis (P<0.01, OR 2.305, 95% CI: 1.285-4.132), late onset of disease (P<0.01, OR 2.542, 95% CI: 1.266-5.102), familial psoriasis (P<0.02, OR 2.220, 95% CI: 1.249-3.945), and sporadic disease (P<0.01, OR 2.523, 95% CI: 1.390-4.580). Our data indicate that IL-20 gene polymorphisms should have a role in determining susceptibility to plaque-type psoriasis. The possible role of the studied SNPs in the regulation of the expression of IL-20 is unknown yet and needs further studies."
],
"offsets": [
[
84,
1367
]
]
}
] | [
{
"id": "531d9f14-559e-4b62-9356-119cde65b296",
"type": "gene",
"text": [
"interleukin-20"
],
"offsets": [
[
22,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "6cb0718a-4d65-43a1-b369-b0df21cf80df",
"type": "gene",
"text": [
"IL-20"
],
"offsets": [
[
285,
290
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "42d26fbd-4b0b-4a95-b763-0d73367c4934",
"type": "gene",
"text": [
"IL-20"
],
"offsets": [
[
285,
290
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "1ca160ee-6ae5-4696-9a48-92ba204d9122",
"type": "gene",
"text": [
"HT3"
],
"offsets": [
[
703,
706
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "144125"
}
]
},
{
"id": "06c6eb7e-086b-4cf1-b072-09bee108642f",
"type": "gene",
"text": [
"HT3"
],
"offsets": [
[
703,
706
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "144125"
}
]
},
{
"id": "faa39339-3be3-4ba1-9543-d43f6048aa1d",
"type": "gene",
"text": [
"IL-20"
],
"offsets": [
[
285,
290
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "00d3c497-5bcc-48be-b8f7-c098c399be95",
"type": "gene",
"text": [
"IL-20"
],
"offsets": [
[
285,
290
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "50604"
}
]
},
{
"id": "2f9bb812-fd3f-42c7-9acb-578e3004e596",
"type": "variant",
"text": [
"rs 2981572"
],
"offsets": [
[
173,
183
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2981572"
}
]
},
{
"id": "5f2dfc08-c798-4458-a77d-c941d8bd56ee",
"type": "variant",
"text": [
"rs 2981573"
],
"offsets": [
[
194,
204
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2981573"
}
]
},
{
"id": "49f413d5-88a9-4350-b2a9-58229af82258",
"type": "variant",
"text": [
"rs 2232360"
],
"offsets": [
[
215,
225
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2232360"
}
]
},
{
"id": "d450daf7-ddda-487b-9ef3-15080c679a96",
"type": "variant",
"text": [
"rs 1518108"
],
"offsets": [
[
240,
250
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1518108"
}
]
},
{
"id": "83a407f4-e8ee-4daf-bfd1-915b56b81a85",
"type": "variant",
"text": [
"G allele at position -1053"
],
"offsets": [
[
397,
423
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2981572"
}
]
}
] | [] | [] | [] |
16 | 14715843 | [
{
"id": "2ed1a920-e155-4415-a398-51997fd31dda",
"type": "title",
"text": [
"Ghrelin receptor gene : identification of several sequence variants in extremely obese children and adolescents, healthy normal-weight and underweight students, and children with short normal stature."
],
"offsets": [
[
0,
200
]
]
},
{
"id": "f770c944-728e-4daf-8861-dd068edaf965",
"type": "abstract",
"text": [
"GH secretagogue receptor (GHSR, ghrelin receptor) is involved in regulation of body weight and GH secretion. We initially analyzed two single-nucleotide polymorphisms of the GHSR in up to 184 extremely obese children and adolescents and up to 184 healthy underweight students. The frequency of the 171T allele of rs495225 was higher in our obese samples (75.0%) than in the underweight individuals (70.2%; nominal P = 0.14). This trend could not be substantiated in an additional association study in 270 obese and 145 underweight and normal weight individuals and in a transmission disequilibrium test based on 387 obesity trios (transmission rate of 171T , 51.8%; nominal P = 0.53). Additionally, the coding region of GHSR was systematically screened, and seven sequence variants were identified in 93 obese, 96 normal weight, and 94 underweight individuals and 43 children with short normal stature (SNS). Five silent single-nucleotide polymorphisms showed similar genotype frequencies in the different weight groups and SNS children (all nominal P > 0.3). Two novel missense variants were detected only in one obese carrier and one SNS child, respectively. In conclusion, we did not obtain conclusive evidence for an involvement of the ghrelin receptor gene in body weight regulation or SNS in our study groups."
],
"offsets": [
[
201,
1526
]
]
}
] | [
{
"id": "28745f89-8c15-41a9-93e0-35f598700452",
"type": "gene",
"text": [
"GH secretagogue receptor (GHSR, ghrelin receptor)"
],
"offsets": [
[
201,
250
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2693"
}
]
},
{
"id": "2ef8b153-26e5-4c3d-8bcc-9eaf9ae02d2b",
"type": "gene",
"text": [
"GHSR"
],
"offsets": [
[
227,
231
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2693"
}
]
},
{
"id": "4f2286f6-8c3d-48c7-874e-244be046c92f",
"type": "gene",
"text": [
"GHSR"
],
"offsets": [
[
227,
231
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2693"
}
]
},
{
"id": "f6e8489f-4484-4e67-818d-9631227b9ea6",
"type": "variant",
"text": [
"171T"
],
"offsets": [
[
503,
507
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "495225"
}
]
},
{
"id": "9b54c655-0b53-4afa-8cc1-304074353dad",
"type": "variant",
"text": [
"rs495225"
],
"offsets": [
[
520,
528
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "495225"
}
]
},
{
"id": "ee7993d1-7321-465d-9414-9817e9685141",
"type": "variant",
"text": [
"171T"
],
"offsets": [
[
503,
507
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "495225"
}
]
}
] | [] | [] | [] |
17 | 14715845 | [
{
"id": "42c05b4c-6e3a-49cc-9c1e-de200d2daed1",
"type": "title",
"text": [
"Cytotoxic T lymphocyte-associated molecule-4 polymorphism and relapse of Graves' hyperthyroidism after antithyroid withdrawal."
],
"offsets": [
[
0,
127
]
]
},
{
"id": "3d218e56-12df-40f8-8d3c-2855ca13d4ff",
"type": "abstract",
"text": [
"We studied the A/G single nucleotide polymorphism (SNP) at position 49 in exon 1 of the cytotoxic T lymphocyte-associated molecule-4 gene in 148 Chinese Graves' disease (GD) patients and 171 controls. Our primary aim was to test for the association of this SNP with the relapse of the hyperthyroidism after antithyroid withdrawal. Our secondary aim was to investigate the relationship between GD patients and controls according to the SNP genotypes. All GD patients were divided into the following three groups according to the time of relapse after drug discontinuation: group 1, early relapse within 9 months; group 2, relapse between 10 and 36 months; and group 3, relapse 3 or more years after discontinuation of treatment. There was a significant difference of genotype frequencies (P < 0.001) and allele frequencies (P < 0.001) among the three groups of patients. The frequency of the G/G genotype decreased from 79% to 64% and 39% in groups 1, 2, and 3, respectively. Compared with controls, a strong association (P < 0.001) of G allele was found for group 1, and moderate significance (P = 0.04) was found for group 2, but no association (P = 0.33) was found for group 3. At the end of treatment, the percentage of patients with persistent TSH-receptor antibody was statistically different (A/A, 9.0%; A/G, 20.8%; G/G, 45.5%; P = 0.004). Using 3 yr as the cutoff point for multivariate logistic regression analysis, we found that the G/G genotype (adjusted odds ratio, 3.1 compared with A/G plus A/A; 95% confidence interval, 1.3-7.1), larger goiter size at the end of treatment, and positive TSH-receptor antibody at the end of treatment were independent risk factors of recurrence. We conclude that the A/G polymorphism of the cytotoxic T lymphocyte-associated molecule-4 gene affects the progress of GD. The G/G genotype is associated with poor outcome."
],
"offsets": [
[
128,
1998
]
]
}
] | [
{
"id": "e4dc7f4f-6db8-4b3e-b2df-5978d447d1a9",
"type": "gene",
"text": [
"cytotoxic T lymphocyte-associated molecule-4"
],
"offsets": [
[
219,
263
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1493"
}
]
},
{
"id": "ba5bbf44-9023-4e76-829b-9cccd8e6fbf1",
"type": "gene",
"text": [
"cytotoxic T lymphocyte-associated molecule-4"
],
"offsets": [
[
219,
263
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1493"
}
]
},
{
"id": "56a3e6c2-93f9-4a4e-ae91-0b7b6d543a7c",
"type": "variant",
"text": [
"A/G single nucleotide polymorphism (SNP) at position 49"
],
"offsets": [
[
144,
199
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "231775"
}
]
}
] | [] | [] | [] |
18 | 14729863 | [
{
"id": "7f8aa479-4638-48cb-b473-c6bdc51aabac",
"type": "title",
"text": [
"APOA5 gene variants, lipoprotein particle distribution, and progression of coronary heart disease: results from the LOCAT study."
],
"offsets": [
[
0,
129
]
]
},
{
"id": "acd21656-6eda-4ca0-8c73-9338f5e1928a",
"type": "abstract",
"text": [
"Animal and human studies support a role for apolipoprotein A-V (apoA-V) in triglyceride (TG) metabolism. We examined the relationship of APOA5 -1131T>C and S19W with lipid subfractions and progression of atherosclerosis in the Lopid Coronary Angiography Trial. Compared with -1131TT men (n = 242), carriers of the -1131C allele (n = 54) had significantly higher total TG (P = 0.03), reflected in significantly increased VLDL mass [higher VLDL-TG, VLDL-cholesterol, VLDL-protein, and surface lipids (all P < 0.05)]. Because apoB levels were unaffected by genotype, this suggests an increase in VLDL size and not number. Compared with 19SS men (n = 268), 19W carriers (n = 44) had higher intermediate density lipoprotein (IDL)-TG, IDL-cholesterol (P = 0.04), and IDL-surface components [free cholesterol (P = 0.005) and phospholipids (P = 0.017)] but not protein content, suggesting an increase in IDL lipid enrichment resulting in an increase in IDL size. 19W carriers also showed a trend toward increased progression of atherogenesis, as measured by change in average diameter of segments (-0.46 +/- 0.011 mm compared with -0.016 +/- 0.006 mm) in 19SS men (P = 0.08). There was no effect of genotype on the response of these parameters to gemfibrozil treatment. These results shed new light on the role of APOA5 variants in TG metabolism and coronary heart disease risk."
],
"offsets": [
[
130,
1524
]
]
}
] | [
{
"id": "a210476d-ced4-4fab-9672-d4b24ced3c2b",
"type": "gene",
"text": [
"apolipoprotein A-V (apoA-V)"
],
"offsets": [
[
175,
202
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "116519"
}
]
},
{
"id": "45f3b05a-3424-42ec-b739-8f3d68fbb921",
"type": "gene",
"text": [
"APOA5"
],
"offsets": [
[
0,
5
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "116519"
}
]
},
{
"id": "17028a9f-6a8c-4216-adbb-5d554fdd911e",
"type": "gene",
"text": [
"apoB"
],
"offsets": [
[
666,
670
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "338"
}
]
},
{
"id": "7f9ecd2e-8a8b-4dfd-83e9-03a578b5b4b6",
"type": "gene",
"text": [
"APOA5"
],
"offsets": [
[
0,
5
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "116519"
}
]
},
{
"id": "737d17c8-4c65-4d02-ade5-ebaf8af5805c",
"type": "variant",
"text": [
"-1131T>C"
],
"offsets": [
[
278,
286
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T-1131C"
}
]
},
{
"id": "76ad8332-6872-48a6-af09-b486e827fd04",
"type": "variant",
"text": [
"S19W"
],
"offsets": [
[
293,
297
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
},
{
"id": "1ec09e72-2972-42ba-bf78-08ac1df18900",
"type": "variant",
"text": [
"-1131TT"
],
"offsets": [
[
414,
421
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T-1131T"
}
]
},
{
"id": "0afb498a-eee1-4996-a8d7-46c0d2a1f9f0",
"type": "variant",
"text": [
"-1131C"
],
"offsets": [
[
455,
461
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-1131C"
}
]
},
{
"id": "5c3af14c-65c9-439b-8b89-efa2854aaee7",
"type": "variant",
"text": [
"19SS"
],
"offsets": [
[
778,
782
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
},
{
"id": "72541488-40be-4c8e-9a45-ed6a19e55a9e",
"type": "variant",
"text": [
"19W"
],
"offsets": [
[
294,
297
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
},
{
"id": "7da432db-a1df-403a-8335-5133216a7b40",
"type": "variant",
"text": [
"19W"
],
"offsets": [
[
294,
297
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
},
{
"id": "fd50f843-142f-425f-bf64-5e8b73386044",
"type": "variant",
"text": [
"19SS"
],
"offsets": [
[
778,
782
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3135506"
}
]
}
] | [] | [] | [] |
19 | 14730381 | [
{
"id": "8adbde8d-e5b5-4c58-8905-353deb03df8d",
"type": "title",
"text": [
"Association of the Pro12Ala and C1431T 1431T variants of PPARG and their haplotypes with susceptibility to Type 2 diabetes."
],
"offsets": [
[
0,
130
]
]
},
{
"id": "f8374098-8b9c-4502-85fe-b431315678b7",
"type": "abstract",
"text": [
"AIMS/HYPOTHESIS: The Pro12Ala polymorphism of peroxisome proliferator-activated receptor (PPAR)gamma has been consistently associated with Type 2 diabetes. The rare Ala12 variant is estimated to reduce the risk of developing Type 2 diabetes by 20 percent. This variant is in linkage disequilibrium with another common variant, T1431 . Both have opposing associations with body weight. We therefore examined the association of specific haplotypes marked by these two variants with susceptibility to Type 2 diabetes. METHODS: We determined the PPARG genotype of a large Scottish cohort of Type 2 diabetic patients ( n=1997) and compared allele frequencies with a cohort of local children ( n=2444) and a middle-aged, population-based cohort from Scotland ( n=1061). RESULTS: Frequency of the Ala12 allele was slightly lower in the Type 2 diabetic cohort than in the children [odds ratio (OR)=0.91, p=0.1]. In contrast, the Ala12 variant was under-represented in the Type 2 diabetic population when compared with similarly aged non-diabetic adults (OR=0.74, p=0.0006). When the Ala12 variant was on a haplotype not bearing the 1431T variant, it conferred greater protection (OR=0.66, p=0.003). However, when it was present in haplotypes containing the 1431T variant (70% of Ala12 carriers), this protection was absent (OR=0.99, p=0.94). CONCLUSIONS/INTERPRETATION: We replicated the finding that the Ala12 variant of PPARgamma affords protection from Type 2 diabetes, and suggest that this protection is modulated by additional common variation at the PPARG locus."
],
"offsets": [
[
131,
1717
]
]
}
] | [
{
"id": "fd5912c7-23c8-4538-95b0-ebda91d0c5ef",
"type": "gene",
"text": [
"peroxisome proliferator-activated receptor (PPAR)gamma"
],
"offsets": [
[
180,
234
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "9b2a873b-47da-4248-aaca-eac2ffa99659",
"type": "gene",
"text": [
"PPARG"
],
"offsets": [
[
63,
68
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "ae6140a7-b4ba-423c-87d4-6bffedbabc55",
"type": "gene",
"text": [
"PPARG"
],
"offsets": [
[
63,
68
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5468"
}
]
},
{
"id": "4d4e46af-78b1-4d90-a6c2-39358c4c2e1a",
"type": "variant",
"text": [
"Pro12Ala"
],
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[
20,
28
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "91f5b4c5-7ebb-47a9-a91b-d055c66651a5",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "83a65aca-5d4d-4554-8402-26aa72798de2",
"type": "variant",
"text": [
"T1431"
],
"offsets": [
[
465,
470
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3856806"
}
]
},
{
"id": "ba18adb8-58a9-40a7-91a5-dee64414888a",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "08aa0dd9-ca1c-42ad-aaec-d2f8217723c5",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "73847687-d84a-4a59-a21c-6598214a15fb",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "67d1f9ac-b5da-40c5-ad43-3583172c73eb",
"type": "variant",
"text": [
"1431T"
],
"offsets": [
[
36,
41
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3856806"
}
]
},
{
"id": "2620a580-49d6-47df-b12f-23f8ad44dbbb",
"type": "variant",
"text": [
"1431T"
],
"offsets": [
[
36,
41
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3856806"
}
]
},
{
"id": "3f196b22-74df-4194-a7e1-5e515ca473aa",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
},
{
"id": "557d6b01-3331-4e5e-acdd-47992c069ceb",
"type": "variant",
"text": [
"Ala12"
],
"offsets": [
[
301,
306
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1801282"
}
]
}
] | [] | [] | [] |
20 | 14734460 | [
{
"id": "da27afa4-64c7-4d8f-9c0e-15f48773202f",
"type": "title",
"text": [
"Associations between breast cancer susceptibility gene polymorphisms and clinicopathological features."
],
"offsets": [
[
0,
102
]
]
},
{
"id": "1af3e59e-b4fe-4622-a2f4-648a563a27a2",
"type": "abstract",
"text": [
"PURPOSE: Genetic polymorphisms may affect not only cancer development but also cancer progression, and as a result could influence cancer phenotypes. The aim of this study was to examine the relationship between breast cancer susceptibility gene polymorphisms and clinicopathological features. Experimental Design: We genotyped 664 Korean primary breast cancer patients for 17 single-nucleotide polymorphisms (SNPs) in nine genes, using a high-throughput SNP scoring method. RESULTS: CYP1A1 codon 462 Ile/Val or Val/Val variants and the CYP1B1 codon 432 Leu/Val variant were found more in breast cancer patients </=35 years of age at onset than the common homozygote [odds ratio (OR), 1.6 and 1.7, respectively]. In combination analysis of these two SNPs, the OR was 1.9 when one of them was heterozygous or a rare homozygous form, and increased to 2.3 when both were variants (P = 0.006). Cases with Ile/Val at CYP1A1 codon 462 CYP1A1 codon 462 were 2.6-fold and those with Val/Val were 5.1-fold more likely to have first-degree relatives with breast cancer than those with Ile/Ile (P = 0.002). In the haplotype study of BRCA1 , the 2430C / 2731T / 3667G / 4427C / 4956G homozygote showed less estrogen receptor negativity than the most common diplotype (OR, 0.5; 95% confidence interval, 0.26-0.94). TP53 codon 72 Arg/Pro or Pro/Pro variants were associated with negative axillary lymph node status (OR, 0.7; 95% confidence interval, 0.49-0.94). CONCLUSIONS: These results indicate that polymorphisms of some selected breast cancer susceptibility genes are associated with the clinicopathological phenotypes of breast cancer."
],
"offsets": [
[
103,
1747
]
]
}
] | [
{
"id": "c2a3dc1b-ed5c-48f7-a24c-a9e9acd354d5",
"type": "gene",
"text": [
"CYP1A1"
],
"offsets": [
[
588,
594
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1543"
}
]
},
{
"id": "fd200323-d0b3-46cc-b5ad-8c6cfb9176a1",
"type": "gene",
"text": [
"CYP1B1"
],
"offsets": [
[
645,
651
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1545"
}
]
},
{
"id": "48ccac7d-8d3b-4c03-9652-0ee8f47fef0e",
"type": "gene",
"text": [
"CYP1A1"
],
"offsets": [
[
588,
594
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1543"
}
]
},
{
"id": "761068da-3175-47fb-a3eb-e422f6accb58",
"type": "gene",
"text": [
"BRCA1"
],
"offsets": [
[
1236,
1241
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "672"
}
]
},
{
"id": "87c790be-9268-4346-9984-2f65f7ffa52a",
"type": "gene",
"text": [
"TP53"
],
"offsets": [
[
1419,
1423
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7157"
}
]
},
{
"id": "3b14af26-bef0-4a79-9e27-fea6e985a037",
"type": "variant",
"text": [
"462 Ile/Val"
],
"offsets": [
[
603,
614
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1048943"
}
]
},
{
"id": "6457d11e-48f6-4bbd-a941-3aad744db040",
"type": "variant",
"text": [
"432 Leu/Val "
],
"offsets": [
[
660,
672
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1056836"
}
]
},
{
"id": "b3fc5792-04b8-44a8-92ba-fae3d86cf17a",
"type": "variant",
"text": [
"Ile/Val at CYP1A1 codon 462"
],
"offsets": [
[
1013,
1040
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1048943"
}
]
},
{
"id": "46e62ba5-6d7a-4187-b680-c27af26d67b5",
"type": "variant",
"text": [
"2430C"
],
"offsets": [
[
1249,
1254
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "430C"
}
]
},
{
"id": "38850e3e-39d9-481f-88af-105d4937a67a",
"type": "variant",
"text": [
"2731T"
],
"offsets": [
[
1257,
1262
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "2731T"
}
]
},
{
"id": "ab4a81a2-22fc-44da-a685-835436e8fa90",
"type": "variant",
"text": [
"3667G"
],
"offsets": [
[
1265,
1270
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "3667G"
}
]
},
{
"id": "f0a8e7e5-941d-4690-94e5-44280c364a8f",
"type": "variant",
"text": [
"4427C"
],
"offsets": [
[
1273,
1278
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "4427C"
}
]
},
{
"id": "0ab51732-2e72-40c5-98c4-30f4c7ed46a9",
"type": "variant",
"text": [
"4956G"
],
"offsets": [
[
1281,
1286
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1799967"
}
]
},
{
"id": "cc7ba621-5b71-4160-895f-7b0cc78ab2df",
"type": "variant",
"text": [
"72 Arg/Pro"
],
"offsets": [
[
1432,
1442
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1042522"
}
]
}
] | [] | [] | [] |
21 | 14737097 | [
{
"id": "fff8f195-db1f-480f-b962-fbc895418580",
"type": "title",
"text": [
"Both risk alleles for FcgammaRIIA and FcgammaRIIIA are susceptibility factors for SLE: a unifying hypothesis."
],
"offsets": [
[
0,
113
]
]
},
{
"id": "2ade9b7f-bc6c-48d3-a367-180b9cf7e8a9",
"type": "abstract",
"text": [
"The aim of this study was to analyze in families with SLE for the presence of linkage and the structure and transmission of haplotypes containing alleles for the low-affinity Fcgamma receptors. The Fcgamma receptor polymorphisms FcgammaRIIA - 131R/H , FcgammaRIIIA - 176F/V and FcgammaRIIIB- NA1/2 and a polymorphism in the FcgammaRIIB gene were genotyped with RFLP, allele-specific PCR or pyrosequencing. Individual SNPs and haplotypes were tested for linkage in multicase families and for association using contingency tables, transmission disequilibrium test and affected family-based control groups in Swedish and Mexican single-case families. No linkage or association could be detected using the FcgammaR polymorphisms in the multicase families. However, an association was found for both FcgammaRIIA - 131R and IIIA- 176F alleles in the single-case families, but not for IIIB or IIB. Allelic association to SLE was found for a haplotype that included both risk alleles, but not in haplotypes where only one or the other was present. We propose that FcgammaRIIA - 131R and FcgammaRIIIA - 176F are both risk alleles for SLE transmitted primarily, but not exclusively on a single major haplotype that behaves functionally in a situation similar to that of compound heterozygozity."
],
"offsets": [
[
114,
1409
]
]
}
] | [
{
"id": "d8f2cceb-b181-4358-9edd-21fae69316d5",
"type": "gene",
"text": [
"FcgammaRIIA"
],
"offsets": [
[
23,
34
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2212"
}
]
},
{
"id": "a5cf0a95-5ccb-4d2e-942f-20ffbd0e4401",
"type": "gene",
"text": [
"FcgammaRIIIA"
],
"offsets": [
[
41,
53
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2214"
}
]
},
{
"id": "17d18ed9-170a-42d3-9d0d-ef0ba06b597f",
"type": "gene",
"text": [
"FcgammaRIIA"
],
"offsets": [
[
23,
34
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2212"
}
]
},
{
"id": "8c111e44-c182-44df-a613-4f00559fd82e",
"type": "gene",
"text": [
"FcgammaRIIA"
],
"offsets": [
[
23,
34
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2212"
}
]
},
{
"id": "ac290a6c-bcbf-4fee-80af-614ef93cbeba",
"type": "gene",
"text": [
"FcgammaRIIIA"
],
"offsets": [
[
41,
53
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2214"
}
]
},
{
"id": "9134e287-afb8-4279-9e10-32f8c322494f",
"type": "variant",
"text": [
"131R/H"
],
"offsets": [
[
358,
364
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "R131H"
}
]
},
{
"id": "cabe6fc6-186b-4d9f-984e-9e54ee1e067d",
"type": "variant",
"text": [
"176F/V"
],
"offsets": [
[
383,
389
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "F176V"
}
]
},
{
"id": "16f9b2e8-f634-4f97-bf3e-3e97f699a2c3",
"type": "variant",
"text": [
"NA1/2 "
],
"offsets": [
[
409,
415
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "a7b4148d-60bf-4e47-9cff-b4422c67b99e",
"type": "variant",
"text": [
"131R"
],
"offsets": [
[
358,
362
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "131R"
}
]
},
{
"id": "73efdf72-a666-45e9-81e7-6a464bf2c8ae",
"type": "variant",
"text": [
"176F"
],
"offsets": [
[
383,
387
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "176F"
}
]
},
{
"id": "aa8f66cd-e2a9-47d6-813e-a4c09db3dfbb",
"type": "variant",
"text": [
"131R"
],
"offsets": [
[
358,
362
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "131R"
}
]
},
{
"id": "81060b1a-1270-4fb0-b9ce-7cb0e1f288e5",
"type": "variant",
"text": [
"176F"
],
"offsets": [
[
383,
387
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "176F"
}
]
}
] | [] | [] | [] |
22 | 14739420 | [
{
"id": "05949769-c3d5-4f53-83c5-5affd2db49bb",
"type": "title",
"text": [
"Collagen type I alpha2 ( COL1A2 ) is the susceptible gene for intracranial aneurysms."
],
"offsets": [
[
0,
86
]
]
},
{
"id": "ede4ef5d-451f-4904-8cb7-e97bf4c80b86",
"type": "abstract",
"text": [
"BACKGROUND AND PURPOSE: The collagen alpha2(I) gene ( COL1A2 ) on chromosome 7q22.1, a positional and functional candidate for intracranial aneurysm (IA), was extensively screened for susceptibility in Japanese IA patients. METHODS: Twenty-one single nucleotide polymorphisms (SNPs) of COL1A2 were genotyped in genomic DNA from 260 IA patients (including 115 familial cases) (mean age, 59.9 years) and 293 controls (mean age, 61.6 years). Differences in allelic and genotypic frequencies between the patients and controls were evaluated with the chi(2) test. Circular dichroism spectrometry was monitored with collagen-related peptides that mimic triple-helical models of type I collagen with Ala-459 and Pro-459 to estimate the conformation and stability of alterations. RESULTS: Significant genotypic association in the dominant model was observed between an exonic SNP of COL1A2 and familial IA patients (chi(2)=11.08; df=1; P=0.00087; odds ratio=3.19; 95% CI, 2.22 to 6.50). This SNP induces Ala to Pro substitution at amino acid 459 , located on a triple-helical domain. Circular dichroism spectra showed that the Pro-459 peptide had a higher thermal stability than the Ala-459 peptide. CONCLUSIONS: The variant of COL1A2 could be a genetic risk factor for IA patients with family history."
],
"offsets": [
[
87,
1398
]
]
}
] | [
{
"id": "985c5793-1540-40c5-828b-a2690688f84b",
"type": "gene",
"text": [
"collagen alpha2(I) gene"
],
"offsets": [
[
116,
139
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "2889a694-e0ad-4854-8648-07273ccebfec",
"type": "gene",
"text": [
"COL1A2"
],
"offsets": [
[
26,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "218ba7ce-1237-4fc3-8536-6ca7ca3c200a",
"type": "gene",
"text": [
"COL1A2"
],
"offsets": [
[
26,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "19f669a5-b2be-4803-880f-aece2bf253f5",
"type": "gene",
"text": [
"COL1A2"
],
"offsets": [
[
26,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "0ec5364f-83f3-440a-b165-e77693ef4986",
"type": "gene",
"text": [
"COL1A2"
],
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[
26,
32
]
],
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{
"db_name": "NCBI Gene",
"db_id": "1278"
}
]
},
{
"id": "c1794ba7-a18f-4749-9d82-d02ce196485e",
"type": "variant",
"text": [
"Ala-459"
],
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[
785,
792
]
],
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{
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"db_id": "459A"
}
]
},
{
"id": "262880e7-24d4-4223-9a24-7cf5475442b1",
"type": "variant",
"text": [
"Pro-459"
],
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799,
806
]
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"db_id": "459P"
}
]
},
{
"id": "6885cbba-ee98-4f7a-8bca-99a84f1e78e5",
"type": "variant",
"text": [
"Ala to Pro substitution at amino acid 459"
],
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1094,
1135
]
],
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{
"id": "a39f883c-5127-4e7b-a496-aac55dfe62a7",
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},
{
"id": "6aa82973-f4ab-44f8-bd97-55e7a56c2e5c",
"type": "variant",
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"Ala-459"
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785,
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],
"normalized": [
{
"db_name": "HGVS-like",
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}
]
}
] | [] | [] | [] |
23 | 14742985 | [
{
"id": "5df219a7-e20c-4f53-9ac7-0080841e5a3e",
"type": "title",
"text": [
"Relationship between postrenal transplant osteonecrosis of the femoral head and gene polymorphisms related to the coagulation and fibrinolytic systems in Japanese subjects."
],
"offsets": [
[
0,
172
]
]
},
{
"id": "2e514b49-6702-49d2-9f76-58995483ae75",
"type": "abstract",
"text": [
"BACKGROUND: Nontraumatic osteonecrosis of the femoral head (ONFH) is one of the complications that may occur after renal transplantation. We investigated the relationship between the incidence of ONFH and polymorphisms in the genes for plasminogen activator inhibitor (PAI)-1 , which is one of the major regulatory proteins of the fibrinolytic system, and 5,10-methylenetetrahydrofolate reductase ( MTHFR ), which is associated with the plasma levels of homocysteine in Japanese subjects. METHODS: Thirty-one patients with postrenal transplant ONFH and 106 patients without ONFH were selected. Genotypes of PAI-1 4G/5G and MTHFR C677T were determined by direct sequencing of genomic DNA. In addition, plasma PAI-1 antigen (Ag) levels and plasma total homocysteine (tHcy) levels at the steady state were measured. The relationships between the incidence of ONFH and these genotypes, as well as plasma levels of the gene products, were investigated. RESULTS: Plasma PAI-1 Ag levels were the highest in patients with the 4G/4G genotype, and plasma tHcy levels were the highest in patients with TT genotypes of MTHFR C677T . However, the relationship between the incidence of ONFHH and PAI-1 4G/5G or MTHFR C677T was not observed. The relationship between the incidence of ONFH and plasma levels of PAI-1 Ag or tHcy was not observed. CONCLUSIONS: Genotypes of PAI-1 4G/5G and MTHFR C677T or plasma concentrations of PAI-1 Ag and tHcy had no effect on the incidence of ONFH in Japanese subjects, unlike the results of studies performed in white subjects. The effect of genetic background on the pathologic conditions that developed in patients with postrenal transplant ONFH may differ according to race."
],
"offsets": [
[
173,
1910
]
]
}
] | [
{
"id": "35310ea0-c58c-480e-ba33-498f95d7ecc4",
"type": "gene",
"text": [
"plasminogen activator inhibitor (PAI)-1"
],
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[
410,
449
]
],
"normalized": [
{
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"db_id": "5054"
}
]
},
{
"id": "1e3f0f2d-dbde-40af-9807-51877de75b41",
"type": "gene",
"text": [
"5,10-methylenetetrahydrofolate reductase"
],
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531,
571
]
],
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}
]
},
{
"id": "da1a87c9-40aa-4404-a47f-0a5b9889c657",
"type": "gene",
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"MTHFR"
],
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575,
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]
],
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}
]
},
{
"id": "3fee8bf6-3872-4d4d-a1b3-42b1751bb418",
"type": "gene",
"text": [
"PAI-1"
],
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[
784,
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]
],
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}
]
},
{
"id": "697f6168-3742-4c4f-940d-d01e5b12fd9a",
"type": "gene",
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"MTHFR"
],
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[
575,
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]
],
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"db_id": "4524"
}
]
},
{
"id": "c711c658-67df-4cd3-944d-2edac3eb9d13",
"type": "gene",
"text": [
"PAI-1"
],
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[
784,
789
]
],
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{
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}
]
},
{
"id": "5f18a62a-30cd-47f6-9077-0b7fc6a5954a",
"type": "gene",
"text": [
"PAI-1"
],
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[
784,
789
]
],
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{
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}
]
},
{
"id": "57f88726-de23-47be-badb-9b03757e41ec",
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"MTHFR"
],
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575,
580
]
],
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}
]
},
{
"id": "48da086c-6eb6-4582-921c-8b7f76c761f9",
"type": "gene",
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"PAI-1"
],
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784,
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]
],
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}
]
},
{
"id": "9cb9c464-20be-4fc7-8d86-de7bf6780c51",
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"MTHFR"
],
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575,
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]
],
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]
},
{
"id": "8e1bcb8c-7737-4923-a50e-dbadfcbd30ca",
"type": "gene",
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"PAI-1"
],
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784,
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]
],
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}
]
},
{
"id": "87ec1487-5c88-46a0-ba7e-e5fceda715c6",
"type": "gene",
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"PAI-1"
],
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784,
789
]
],
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}
]
},
{
"id": "ec147ead-1b11-48f4-a8f2-b2479ae3a7fc",
"type": "gene",
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"MTHFR"
],
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[
575,
580
]
],
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{
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}
]
},
{
"id": "316f3231-2388-46f8-877e-5bcc67f06dc8",
"type": "gene",
"text": [
"PAI-1"
],
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[
784,
789
]
],
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{
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"db_id": "5054"
}
]
},
{
"id": "d9f38159-0fe2-438b-8e2c-14e5120596e1",
"type": "variant",
"text": [
"4G/5G"
],
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[
792,
797
]
],
"normalized": [
{
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"db_id": "null"
}
]
},
{
"id": "e3257fa7-361a-4c6c-b016-556ea8349cde",
"type": "variant",
"text": [
"C677T"
],
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[
812,
817
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C677T"
}
]
},
{
"id": "0255381f-0919-4005-ad5b-1d09b60b7368",
"type": "variant",
"text": [
"C677T"
],
"offsets": [
[
812,
817
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C677T"
}
]
},
{
"id": "c45c4142-227a-461c-b484-9e95742bfe22",
"type": "variant",
"text": [
"4G/5G"
],
"offsets": [
[
792,
797
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "875321dd-acd4-4d0e-aa6c-a52e15bca9cf",
"type": "variant",
"text": [
"C677T"
],
"offsets": [
[
812,
817
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C677T"
}
]
},
{
"id": "201aad75-fa1a-4d77-bdd8-1fe24af92112",
"type": "variant",
"text": [
"4G/5G"
],
"offsets": [
[
792,
797
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "38a6b3e6-235f-40a8-b0e4-de212270a5cc",
"type": "variant",
"text": [
"C677T"
],
"offsets": [
[
812,
817
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C677T"
}
]
}
] | [] | [] | [] |
24 | 14747301 | [
{
"id": "0eb288ed-031a-4223-bd62-bcfb75d6df76",
"type": "title",
"text": [
"Uncoupling protein 2 promoter polymorphism -866G/A affects its expression in beta-cells and modulates clinical profiles of Japanese type 2 diabetic patients."
],
"offsets": [
[
0,
160
]
]
},
{
"id": "921ebc61-d950-4c08-bb5e-7d0abaa01a79",
"type": "abstract",
"text": [
"Common uncoupling protein 2 ( UCP2 ) promoter polymorphism -866G/A is reported to be associated with its expression in adipose tissue and the risk of obesity in Caucasians. On the other hand, several studies suggested that UCP2 expression in beta-cells is an important determinant of insulin secretion. In the Japanese population, morbid obesity is very rare, and insulin secretion capacity is relatively low as compared with Caucasians. Because UCP2 would link to insulin secretion and obesity, it might explain this ethnic difference. Here, we report that the UCP2 promoter with the A allele showed higher promoter activity in the INS-1 beta-cell line. The frequency of the A allele is higher in our Japanese study than that in Caucasians. Type 2 diabetic patients with the A allele need insulin therapy earlier and showed higher frequency of insulin treatment. Moreover glucose-induced early insulin secretion is significantly lower in patients with the A allele. However, there was no difference in allele frequency between obese and lean type 2 diabetic patients. In conclusion, UCP2 promoter polymorphism -866G/A does not affect obesity in Japanese type 2 diabetic patients but affects its transcription in beta-cells and modulates glucose-induced insulin secretion and eventually insulin requirement in Japanese type 2 diabetic patients. Higher A allele frequency in the Japanese population might partly explain the ethnic difference of insulin secretion capacity."
],
"offsets": [
[
161,
1662
]
]
}
] | [
{
"id": "1ca3c0f7-9474-4939-9cff-d12ffa747eb4",
"type": "gene",
"text": [
"UCP2"
],
"offsets": [
[
191,
195
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7351"
}
]
},
{
"id": "274c2781-40be-4fdd-8ff2-1cbe0154ec35",
"type": "gene",
"text": [
"UCP2"
],
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[
191,
195
]
],
"normalized": [
{
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}
]
},
{
"id": "e0c4037c-ca5a-41d5-a0b7-3d5d1dcc07de",
"type": "gene",
"text": [
"insulin"
],
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[
450,
457
]
],
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}
]
},
{
"id": "19a42c2a-9eb2-4e39-84dc-095fe5e49b2b",
"type": "gene",
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"insulin"
],
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[
450,
457
]
],
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}
]
},
{
"id": "cef8c0f4-48b7-42b0-ae61-4dee1f48ea04",
"type": "gene",
"text": [
"UCP2"
],
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[
191,
195
]
],
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}
]
},
{
"id": "0c1d4586-24aa-4296-8d33-4cec6de67cd7",
"type": "gene",
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"insulin"
],
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[
450,
457
]
],
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}
]
},
{
"id": "34b0add5-b6a7-4a9d-90d8-6fd165dc495e",
"type": "gene",
"text": [
"UCP2"
],
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[
191,
195
]
],
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}
]
},
{
"id": "3d3230b8-608e-46b1-9bac-5440e891d87f",
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"insulin"
],
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[
450,
457
]
],
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}
]
},
{
"id": "e8bc33de-e7e0-41b2-8486-31e9ea46e7b0",
"type": "gene",
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"insulin"
],
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[
450,
457
]
],
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{
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}
]
},
{
"id": "6b112fee-58a6-4165-8ac8-40838e81e97b",
"type": "gene",
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"insulin"
],
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[
450,
457
]
],
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{
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}
]
},
{
"id": "fcd77405-3120-4333-9b57-4a841f20dae3",
"type": "gene",
"text": [
"UCP2"
],
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[
191,
195
]
],
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"db_id": "7351"
}
]
},
{
"id": "6f4febaf-874a-471c-8480-0b438d58e56e",
"type": "gene",
"text": [
"insulin"
],
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[
450,
457
]
],
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{
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}
]
},
{
"id": "f2fda696-d5b0-45fe-a9b3-0f7bd598beaa",
"type": "gene",
"text": [
"insulin"
],
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[
450,
457
]
],
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{
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}
]
},
{
"id": "10a3050b-1274-4424-b5a0-f65aad234a8d",
"type": "gene",
"text": [
"insulin"
],
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[
450,
457
]
],
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{
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"db_id": "3630"
}
]
},
{
"id": "fd11b891-a9a6-4130-85a0-d59714e1aca4",
"type": "variant",
"text": [
"-866G/A"
],
"offsets": [
[
45,
52
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
},
{
"id": "1bc07e6b-ba5a-4a9f-9d4a-98c04f8e0284",
"type": "variant",
"text": [
"-866G/A"
],
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[
45,
52
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-866A"
}
]
}
] | [] | [] | [] |
25 | 14749980 | [
{
"id": "78fc68cc-0306-4985-b865-2e1a9f5e39b2",
"type": "title",
"text": [
"Association of TAP2 gene polymorphisms in Chinese patients with rheumatoid arthritis."
],
"offsets": [
[
0,
87
]
]
},
{
"id": "0369aa6c-b8ac-4e92-bde3-0cbbb9b33511",
"type": "abstract",
"text": [
"The aim of this study was to investigate the association between the polymorphism of transporters associated with antigen processing ( TAP1 / TAP2 ) genes and rheumatoid arthritis in Chinese patients. A total of 100 RA patients and 99 healthy control subjects were enrolled. Analyses with polymerase chain reaction (PCR) based restrictions were used to identify the polymorphisms of the TAP1 and TAP2 genes, which were mapped on chromosome 6. There was a significant difference in the distribution of the TAP2 gene codon 565 polymorphism frequency between the RA patients and healthy control subjects ( p<0.001). The odds ratio for the risk of the 'A' allele in RA patients was 1.60 (95% CI: 0.82-2.92). No statistical associations in the distribution of the TAP1 gene polymorphism frequency were found between RA patients and controls. There were some physical links found between TAP1 / TAP2 gene polymorphism loci. However, there was no linkage observed from TAP1 / TAP2 gene polymorphisms and HLA-DRB1*04 between RA patients and healthy controls. We concluded that the TAP2 gene codon 565 'A' allele was associated with RA in Chinese patients in Taiwan. Individuals possessing the 'A' allele had a higher incidence of RA. A lack of association of TAP1 gene polymorphisms between RA patients and healthy individuals was noted. The results of this study provide genetic evidence that TAP2 gene codon 565 polymorphism may play a role in RA."
],
"offsets": [
[
88,
1552
]
]
}
] | [
{
"id": "5b57b373-082e-433a-bab7-9a0fc5782890",
"type": "gene",
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"TAP1"
],
"offsets": [
[
224,
228
]
],
"normalized": [
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}
]
},
{
"id": "1479f5b5-51c0-4c12-bc63-c16c0ca02259",
"type": "gene",
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"TAP2"
],
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[
16,
20
]
],
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{
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}
]
},
{
"id": "72e92a69-a948-4f00-9be4-a9763a693665",
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"TAP1"
],
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224,
228
]
],
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}
]
},
{
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],
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16,
20
]
],
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}
]
},
{
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16,
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],
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}
]
},
{
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],
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224,
228
]
],
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}
]
},
{
"id": "6f6582db-eae8-4620-ae5b-d8c0e72ff5b8",
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"text": [
"TAP1"
],
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224,
228
]
],
"normalized": [
{
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}
]
},
{
"id": "20d4499e-0d77-493a-882d-afdb1c19730d",
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"text": [
"TAP2"
],
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16,
20
]
],
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"db_id": "6891"
}
]
},
{
"id": "b138e724-c5b5-410f-b114-ad20400d0ca4",
"type": "gene",
"text": [
"TAP1"
],
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224,
228
]
],
"normalized": [
{
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}
]
},
{
"id": "4966f8ef-441f-4425-ae2c-7e6a8cb590c4",
"type": "gene",
"text": [
"TAP2"
],
"offsets": [
[
16,
20
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6891"
}
]
},
{
"id": "c494b22d-8241-43db-958a-e193e201b2d4",
"type": "gene",
"text": [
"TAP2"
],
"offsets": [
[
16,
20
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6891"
}
]
},
{
"id": "bf9a77f0-df58-4a60-8c7b-45b8fb8ad87e",
"type": "gene",
"text": [
"TAP1"
],
"offsets": [
[
224,
228
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6890"
}
]
},
{
"id": "e0af70a0-b74e-4ac1-ad29-8193cd66019c",
"type": "gene",
"text": [
"TAP2"
],
"offsets": [
[
16,
20
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6891"
}
]
},
{
"id": "d247fb00-9bb9-4cc5-a674-0fb443beff10",
"type": "variant",
"text": [
"HLA-DRB1*04"
],
"offsets": [
[
1099,
1110
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
},
{
"id": "a925fd78-6622-43e1-ac98-4af6d616511c",
"type": "variant",
"text": [
"565 'A' "
],
"offsets": [
[
1195,
1203
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2228396"
}
]
}
] | [] | [] | [] |
26 | 14752243 | [
{
"id": "b51de786-9344-4b07-8ad7-4890e41ff115",
"type": "title",
"text": [
"MDR1 haplotypes modify BEN disease risk: a study in Bulgarian patients with Balkan endemic nephropathy compared to healthy controls."
],
"offsets": [
[
0,
133
]
]
},
{
"id": "c38710f9-6aaf-4d45-9a9e-a59a7b40ce55",
"type": "abstract",
"text": [
"BACKGROUND: Balkan endemic nephropathy (BEN) is a slow progressive nephropathy with frequent occurrence of uroepithelial tumors in the upper urinary tract. Genetic factors involved in xenobiotic detoxification mechanisms may cause genetic predisposition to BEN and influence the risk for this disease. Polymorphic MDR1 variants with decreased P-glycoprotein (P-gp) activity modulate the risk for renal neoplasm. We have therefore investigated the impact of MDR1 polymorphisms on BEN manifestation. METHODS: The constitutional genotype frequencies of two SNPs ( C3435T and G2677T ) in the MDR1 gene in 112 healthy control subjects were investigated and compared with those of 96 patients with BEN. Identification of the SNPs was done with rapid cycle real-time PCR and melting curve analysis with allele-specific probes. RESULTS: The frequency of mutant alleles was comparable in both groups. Significant differences were revealed when the MDR1 haplotypes were analyzed. Individuals with a predicted haplotype 12 (2677G/3435T) were less frequent in BEN cases (frequency 7.3%) than in controls (16.1%, p = 0.006). We found that carriers of the haplotype 12 had a decreased risk for BEN (OR = 0.411; 0.21-0.78). CONCLUSIONS: The data suggest that haplotype 12 is protective against BEN. There is no clear molecular explanation of the MDR1 haplotype effects on the protein activity, which can explain the modified effect of the haplotype 12 on BEN risk."
],
"offsets": [
[
134,
1597
]
]
}
] | [
{
"id": "307f4183-7b82-4d3f-920d-6335ed73ecd5",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "b0c1cc2f-bc09-4b0d-b96e-15d9de9ab401",
"type": "gene",
"text": [
"P-glycoprotein (P-gp)"
],
"offsets": [
[
480,
501
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "2cd7b4b4-a756-4d6d-aff1-b4f5e86c462e",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "79833a71-45a3-40a8-9330-c5687cd0df8e",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "47d365e3-8e6e-4b86-94c8-c08c98c3439d",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "94cf8b69-0db0-40b7-8185-5d6ca10fc200",
"type": "gene",
"text": [
"MDR1"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5243"
}
]
},
{
"id": "b6a2ee46-6ea2-4325-8d0c-b07c26a4fa30",
"type": "variant",
"text": [
"C3435T"
],
"offsets": [
[
701,
707
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1045642"
}
]
},
{
"id": "ba08eb5e-ef68-486a-ba2a-479234857d89",
"type": "variant",
"text": [
"G2677T"
],
"offsets": [
[
714,
720
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2032582"
}
]
}
] | [] | [] | [] |
27 | 14755442 | [
{
"id": "2e350ae6-ed7b-4556-9ec1-1e2d44ad9d88",
"type": "title",
"text": [
"TNXB locus may be a candidate gene predisposing to schizophrenia."
],
"offsets": [
[
0,
66
]
]
},
{
"id": "f4da333a-b734-4850-938f-9abed7db1fc1",
"type": "abstract",
"text": [
"We report here on the detection of nine single nucleotide polymorphisms (SNPs) near to the NOTCH4 locus in the search for schizophrenia susceptibility genes in the class III region of the human major histocompatibility complex (MHC). We totally analyzed 122 family trios recruited in the UK. The TDT analysis demonstrated that of the nine SNPs, three were associated with schizophrenia, including rs1009382 (P = 0.00047), rs204887 (P = 0.007), and rs8283 (P = 0.015). Both rs1009382 and rs204887 are present in the TNXB locus. The rs1009382 is a non-synonymous SNP located in exon 23 of the gene and its A to G base change causes a Glu2578Gly substitution. The goodness-of-fit test showed that genotypic distribution of rs1009382 was deviated from Hardy-Weinberg equilibrium due to homozygote excess in the patient group (P = 0.01), suggesting that a double dose of a genetic risk may be involved. Possibly, rs1009382 is a candidate SNP predisposing to a schizophrenic illness. Moreover, the test for linkage disequilibrium (LD) between paired SNPs showed that the nine SNPs studied may be in the same LD block with an unexpected pattern as the strength of LD was not correlated with the distance between paired SNPs. The haplotype analysis suggested that there might be more than one disease-related allele located in the class III region of the MHC, and that these alleles possibly confer either susceptibility or resistance to schizophrenia."
],
"offsets": [
[
67,
1533
]
]
}
] | [
{
"id": "979e83f7-915a-4b78-9729-8714e25ba13a",
"type": "gene",
"text": [
"NOTCH4"
],
"offsets": [
[
159,
165
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4855"
}
]
},
{
"id": "a6a6e5c7-b0b5-48f4-93bb-f966404764f4",
"type": "gene",
"text": [
"TNXB"
],
"offsets": [
[
0,
4
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7148"
}
]
},
{
"id": "d5cd3e26-6d2b-4c1e-b6c1-6e9214001dc8",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "da664296-83cb-4f27-9382-d906e3306b72",
"type": "variant",
"text": [
"rs204887"
],
"offsets": [
[
494,
502
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "204887"
}
]
},
{
"id": "1dc454fd-64cb-4d31-9b37-e48ba9aa81ee",
"type": "variant",
"text": [
"rs8283"
],
"offsets": [
[
522,
528
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "8283"
}
]
},
{
"id": "f8f854f2-b07d-49dc-a9fa-a1d2a5d2f1f4",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "b8d30d1e-056f-4895-85c1-2838a82a10aa",
"type": "variant",
"text": [
"rs204887"
],
"offsets": [
[
494,
502
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "204887"
}
]
},
{
"id": "27fbea7e-8718-4633-8645-97a6a4a1472f",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "34adcdb1-b9a4-469e-93c3-961e1cf3f2bc",
"type": "variant",
"text": [
"Glu2578Gly"
],
"offsets": [
[
716,
726
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "fee1e9d0-cf18-43fe-955b-aa83585fbe0a",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
},
{
"id": "f523305d-a8f9-48cb-af7d-c9b8f4e175fd",
"type": "variant",
"text": [
"rs1009382"
],
"offsets": [
[
467,
476
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1009382"
}
]
}
] | [] | [] | [] |
28 | 14755445 | [
{
"id": "dce5b786-ef90-40d9-8943-ac5dc8e2b3f5",
"type": "title",
"text": [
"No association between the APOE gene and autism."
],
"offsets": [
[
0,
50
]
]
},
{
"id": "3c31c46e-3b7f-4c5e-b7f4-0322aa3d53b6",
"type": "abstract",
"text": [
"Autism is a neurodevelopmental disorder characterized by stereotypic and repetitive behavior and interests, together with social and communicative deficiencies. The results of several genomic screens suggest the presence of an autism susceptibility locus on chromosome 19p13.2-q13.4. The apolipoprotein E ( APOE ) gene on chromosome 19 encodes for a protein, apoE , whose different isoforms (E2, E3, E4) influence neuronal growth. APOE participates in lipid transport and metabolism, repair, growth, and maintenance of axons and myelin during neuronal development. The APOE protein competes with the Reelin protein for VLDL/ APOE R2 receptor binding. Several studies have reported evidence for an association between autism and the Reelin gene. Based on these data we tested for association between APOE and autism using family-based association methods in a data set of 322 autism families. Three promoter, one intronic, and one 3' UTR single nucleotide polymorphisms (SNPs) in the APOE gene ( -491a/t , -427c/t , -219g/t , 113c/g , and 5361c/t ) as well as the APOE functional polymorphism (E2, E3, E4) were examined and failed to reveal significant evidence that autism is associated with APOE ."
],
"offsets": [
[
51,
1271
]
]
}
] | [
{
"id": "bf24c118-1fd4-47ed-a216-a3d861a3fbd2",
"type": "gene",
"text": [
"apolipoprotein E "
],
"offsets": [
[
340,
357
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "a37bd779-e7e7-4b49-bad0-8359e8cda2f2",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "82817105-0596-4382-b142-049b9678f837",
"type": "gene",
"text": [
"apoE"
],
"offsets": [
[
413,
417
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "c96bb4ea-8419-4625-b276-a09236e8e1aa",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "3937bc2e-7f95-4f9e-aec6-849f2a2c99d9",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "67c1c034-2cb8-4876-9a92-e9d763337ce3",
"type": "gene",
"text": [
"Reelin"
],
"offsets": [
[
659,
665
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5649"
}
]
},
{
"id": "7add8d05-075b-4acc-af0e-490845fffbfd",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "c21f7363-7509-4f74-804d-2be1cc48eacd",
"type": "gene",
"text": [
"Reelin"
],
"offsets": [
[
659,
665
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5649"
}
]
},
{
"id": "2a6aa8b9-eeff-466d-a982-97fc47288b4a",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "d4ab1259-51ac-4095-a7b9-68647dea129a",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "541b5bdb-dba5-4286-aa96-3d03bcabde98",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "5c077cfd-0cff-4d6b-8cc8-040489dc018a",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
28,
32
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "aa7199f9-dae7-4c53-895d-f89b14e6e76f",
"type": "variant",
"text": [
"-491a/t"
],
"offsets": [
[
1061,
1068
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-491T"
}
]
},
{
"id": "e1cae161-5721-4ee0-b842-98def4c8676c",
"type": "variant",
"text": [
"-427c/t"
],
"offsets": [
[
1072,
1079
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-427T"
}
]
},
{
"id": "c0ada70b-2a68-44e4-9c88-999318ae4c5f",
"type": "variant",
"text": [
"-219g/t"
],
"offsets": [
[
1083,
1090
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-219T"
}
]
},
{
"id": "3855b7ca-19f5-4e0d-b868-21346c908d1a",
"type": "variant",
"text": [
"113c/g"
],
"offsets": [
[
1094,
1100
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C113G"
}
]
},
{
"id": "8793094e-2874-49e0-805e-d966510c0ae0",
"type": "variant",
"text": [
"5361c/t"
],
"offsets": [
[
1108,
1115
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C5361T"
}
]
}
] | [] | [] | [] |
29 | 14755451 | [
{
"id": "6e7866bc-4ec0-4536-943c-f7d1a5fe251f",
"type": "title",
"text": [
"No association between the insulin degrading enzyme gene and Alzheimer's disease in a Japanese population."
],
"offsets": [
[
0,
108
]
]
},
{
"id": "2f7da9c6-a9c0-4785-9b90-19c8f84f472b",
"type": "abstract",
"text": [
"Susceptibility to Alzheimer's disease (AD) is thought to be regulated by multiple genetic factors. Recently, three independent studies have reported that loci on chromosome 10q are linked with AD, and the insulin degrading enzyme ( IDE ; MIM 146680) gene located on chromosome 10q23-q25; IDE is located close to the maker D10S583, which exhibits a maximum LOD score for late-onset AD. We examined seven polymorphisms in the IDE gene, the marker D10S583 in the 5' flanking region, and SNPs in introns 1, 3, 11, 20, 21, and 22 ( rs#1999764 , 1855915 , 1970244 , 538469 , 551266 , and 489517 , respectively). Four SNPs in introns 3, 11, 20, and 22 did not exhibit any polymorphisms in the Japanese population that was studied. D10S583 and two SNPs in introns 1 and 21 did not exhibit a significant association with early- or late-onset AD. In addition, no associations were observed for subgroups of AD grouped according to APOE status. The present study indicates that the IDE gene polymorphisms do not confer susceptibility to early- or late-onset AD at least in a Japanese population."
],
"offsets": [
[
109,
1208
]
]
}
] | [
{
"id": "52b0878f-69fc-4e8d-84a0-404a575cd721",
"type": "gene",
"text": [
"insulin degrading enzyme"
],
"offsets": [
[
28,
52
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "1a65d751-af68-41a1-abf6-fa966487c3a3",
"type": "gene",
"text": [
"IDE"
],
"offsets": [
[
343,
346
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "4a0db4f6-8c42-4ac2-bbc6-e92ba5530256",
"type": "gene",
"text": [
"IDE"
],
"offsets": [
[
343,
346
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "6b82ed17-5032-4724-a27d-9bd0e555ad1c",
"type": "gene",
"text": [
"IDE"
],
"offsets": [
[
343,
346
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "2d13d83f-fbab-4228-8e46-a1fa55de2bd0",
"type": "gene",
"text": [
"APOE"
],
"offsets": [
[
1042,
1046
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "348"
}
]
},
{
"id": "42579967-e581-47bd-a8f7-13bfb554fc38",
"type": "gene",
"text": [
"IDE"
],
"offsets": [
[
343,
346
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3416"
}
]
},
{
"id": "8f7e3345-7c70-4cac-8c08-8d89c5ff4858",
"type": "variant",
"text": [
"rs#1999764"
],
"offsets": [
[
642,
652
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1999764"
}
]
},
{
"id": "cf77ee21-03a9-4954-ac25-9773a4cb27f4",
"type": "variant",
"text": [
"1855915"
],
"offsets": [
[
656,
663
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1855915"
}
]
},
{
"id": "f6bc1974-81b5-401c-8fca-7d83c5e9d44e",
"type": "variant",
"text": [
"1970244"
],
"offsets": [
[
667,
674
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1970244"
}
]
},
{
"id": "2581cd8f-aceb-4a3b-997f-7f12088fbac7",
"type": "variant",
"text": [
"538469"
],
"offsets": [
[
678,
684
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "538469"
}
]
},
{
"id": "540eec47-9779-4dc3-8c2e-a59f19eaa9de",
"type": "variant",
"text": [
"551266"
],
"offsets": [
[
688,
694
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "551266"
}
]
},
{
"id": "2cfe5524-fc59-4b3e-bbc9-ecca4f278a03",
"type": "variant",
"text": [
"489517"
],
"offsets": [
[
702,
708
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "489517"
}
]
}
] | [] | [] | [] |
30 | 14764791 | [
{
"id": "479440f6-a6d3-4d95-870e-ede175c4d2e0",
"type": "title",
"text": [
"Common variants in glutamine:fructose-6-phosphate amidotransferase 2 ( GFPT2 ) gene are associated with type 2 diabetes, diabetic nephropathy, and increased GFPT2 mRNA levels."
],
"offsets": [
[
0,
179
]
]
},
{
"id": "a47d80a8-01b8-4e6f-8723-681305f54683",
"type": "abstract",
"text": [
"Increased flux of glucose through the hexosamine biosynthetic pathway has been implicated in insulin resistance, altered insulin secretion, and diabetic nephropathy. Glutamine:fructose-6-phosphate amidotransferase (GFPT) , the rate limiting enzyme in hexosamine biosynthesis, is encoded by the unlinked but highly homologous genes GFPT1 and GFPT2 . We tested the hypothesis that GFPT2 sequence variation contributed to the susceptibility to type 2 diabetes mellitus (T2DM) and diabetic nephropathy in Caucasian and African-American individuals. We identified 11 single nucleotide polymorphisms (SNPs), of which seven were common. A single variant in exon 14, I471V , altered the amino acid sequence, is conserved between human and mouse genes, and was associated with T2DM among Caucasians (P = 0.05). A trend to an association was noted with diabetic nephropathy among African-American individuals (P = 0.15). Several variants in the 3' untranslated region (UTR) and exon 18 were also associated with T2DM in Caucasian individuals (P < 0.05), and the SNP in the 3' UTR was associated with diabetic nephropathy in African-American subjects (P = 0.047). GFPT2 mRNA levels in transformed lymphocytes from study subjects were significantly increased among African-American subjects compared with Caucasian individuals, regardless of diagnosis. Furthermore, the associated allele of the 3' UTR SNP was approximately 2-fold overexpressed. We propose that the 3' UTR variant results in increased GFPT2 mRNA levels with resultant increased hexosamine flux. The I471V variant may contribute to altered protein function or may simply be in linkage disequilibrium with the 3' UTR."
],
"offsets": [
[
180,
1867
]
]
}
] | [
{
"id": "591195b4-1322-4b34-904e-3716fbbfe0cf",
"type": "gene",
"text": [
"insulin"
],
"offsets": [
[
274,
281
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3630"
}
]
},
{
"id": "ea436d0d-cc9f-405e-bad8-41521d59f1a7",
"type": "gene",
"text": [
"insulin"
],
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[
274,
281
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3630"
}
]
},
{
"id": "042c1774-8c8e-484e-b81e-d24e6b263412",
"type": "gene",
"text": [
"Glutamine:fructose-6-phosphate amidotransferase (GFPT)"
],
"offsets": [
[
351,
405
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "29662c65-f4b6-4a77-a932-2817117bf7f4",
"type": "gene",
"text": [
"GFPT1"
],
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[
517,
522
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "2673"
}
]
},
{
"id": "e478e2a7-6884-4ef7-ab7e-b10ec4d01478",
"type": "gene",
"text": [
"GFPT2"
],
"offsets": [
[
73,
78
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "247b8c55-b526-4aff-bf46-54d53004a442",
"type": "gene",
"text": [
"GFPT2"
],
"offsets": [
[
73,
78
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "d6c065a8-e315-4ae4-8fc9-a0d8bf304621",
"type": "gene",
"text": [
"GFPT2"
],
"offsets": [
[
73,
78
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "bb15db1f-d57f-4b59-98b4-2ccd350e37f5",
"type": "gene",
"text": [
"GFPT2"
],
"offsets": [
[
73,
78
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9945"
}
]
},
{
"id": "482d56be-e5f1-4b85-abf1-76a4abe8796e",
"type": "variant",
"text": [
"I471V"
],
"offsets": [
[
850,
855
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2303007"
}
]
},
{
"id": "2da19cb8-2733-4218-a598-80c0910b0115",
"type": "variant",
"text": [
"I471V"
],
"offsets": [
[
850,
855
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2303007"
}
]
}
] | [] | [] | [] |
31 | 14871556 | [
{
"id": "58b6c2f3-70f0-4100-999e-d1f7302341ec",
"type": "title",
"text": [
"KCNJ11 polymorphisms and sudden cardiac death in patients with acute myocardial infarction."
],
"offsets": [
[
0,
92
]
]
},
{
"id": "c5225926-b19b-4416-9320-31c24294b3c1",
"type": "abstract",
"text": [
"PURPOSE: Patients with an acute myocardial infarction (AMI) are of high risk to develop ischemia-induced ventricular arrhythmias, leading to sudden cardiac death (SCD) in about one third of all AMI patients. The individual susceptibility to ischemia-induced arrhythmias may be modified by polymorphisms in genes encoding ion channels. The cardiac ATP-dependent potassium channel (K(ATP)) current is generated by ion channels encoded by the KCNJ11 gene and the SUR2a gene. Opening of the K(ATP) channel during ischemia results in action potential shortening in various studies and may therefore influence the outcome of AMI patients. METHODS: Using a three-primer strategy, we sequenced the complete coding and adjacent 5' and 3' sequences of the intronless KCNJ11 gene (1.3 kb) prospectively in two groups. Patients of group 1 (n = 84) survived three or more transmyocardial infarctions without developing any ventricular arrhythmias. Patients of group 2 died suddenly from their first myocardial infarction (n = 86), most of them witnessed SCDs. RESULTS: We identified a total of six known polymorphisms ( K23E , A190A , L267V , L270V , I337V , and K281K ) and two new polymorphisms ( L267L , 3'UTR +62 G/A ). The allele, genotype, and haplotype frequencies did not differ between the two groups. All polymorphisms were found to be in Hardy-Weinberg equilibrium. In addition, we identified two novel missense mutations in a highly conserved region of the gene in two patients of group 2 ( P266T and R371H ) with yet unknown functional consequences. CONCLUSION: In this study of AMI patients, SCD was not related to polymorphisms in the KCNJ11 gene."
],
"offsets": [
[
93,
1758
]
]
}
] | [
{
"id": "14fdd76a-c70b-475e-8fcf-92228ecf511b",
"type": "gene",
"text": [
"KCNJ11"
],
"offsets": [
[
0,
6
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3767"
}
]
},
{
"id": "460598ef-1edb-41c2-a8d7-80873ac3c756",
"type": "gene",
"text": [
"SUR2a"
],
"offsets": [
[
556,
561
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "10060"
}
]
},
{
"id": "1d4c56f1-2105-4ab3-9637-fd7b503a58b5",
"type": "gene",
"text": [
"KCNJ11"
],
"offsets": [
[
0,
6
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3767"
}
]
},
{
"id": "ff4187a6-e755-4a03-b9a9-f9f248b76c0d",
"type": "gene",
"text": [
"KCNJ11"
],
"offsets": [
[
0,
6
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3767"
}
]
},
{
"id": "21457bdf-09f6-45d5-94e5-be2a48b1c813",
"type": "variant",
"text": [
"K23E"
],
"offsets": [
[
1206,
1210
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5219"
}
]
},
{
"id": "af8f53d9-5561-48f3-a3a7-67a156e48289",
"type": "variant",
"text": [
"A190A"
],
"offsets": [
[
1214,
1219
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5218"
}
]
},
{
"id": "497adc07-d180-43f6-bd79-698a91838c85",
"type": "variant",
"text": [
"L267V"
],
"offsets": [
[
1223,
1228
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "L267V"
}
]
},
{
"id": "07aa494b-5333-4018-8fa5-608d1fc5bd88",
"type": "variant",
"text": [
"L270V"
],
"offsets": [
[
1232,
1237
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1800467"
}
]
},
{
"id": "1be05079-e1f8-4232-a248-c91b92d2155f",
"type": "variant",
"text": [
"I337V"
],
"offsets": [
[
1241,
1246
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5215"
}
]
},
{
"id": "2938acbd-dc01-44d6-ada7-67bed435ab57",
"type": "variant",
"text": [
"K281K"
],
"offsets": [
[
1254,
1259
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "K281K"
}
]
},
{
"id": "a285b1b2-3747-46d9-8242-feb7f49ce21a",
"type": "variant",
"text": [
"L267L"
],
"offsets": [
[
1290,
1295
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "5216"
}
]
},
{
"id": "491ad0b2-57b9-4e6b-a6b2-f655610d8866",
"type": "variant",
"text": [
"3'UTR +62 G/A"
],
"offsets": [
[
1299,
1312
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G62A"
}
]
},
{
"id": "197d0625-933f-4a9b-8d27-d7569226fa79",
"type": "variant",
"text": [
"P266T"
],
"offsets": [
[
1595,
1600
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "P266T"
}
]
},
{
"id": "efe632f6-9212-4038-8972-d683a3db27b9",
"type": "variant",
"text": [
"R371H"
],
"offsets": [
[
1607,
1612
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "R371H"
}
]
}
] | [] | [] | [] |
32 | 14872030 | [
{
"id": "02470daf-ffbd-4ad9-84af-64051fb1261a",
"type": "title",
"text": [
"Functional MxA promoter polymorphism associated with subacute sclerosing panencephalitis."
],
"offsets": [
[
0,
91
]
]
},
{
"id": "9065d996-bfad-420f-a762-9d86a1f34a27",
"type": "abstract",
"text": [
"BACKGROUND: The antivirally active MxA protein is induced by interferon (IFN) alpha/beta and inhibits the replication of single-stranded RNA viruses including measles virus (MV). The authors investigated whether the MxA gene contributed to the development of subacute sclerosing panencephalitis (SSPE) in Japanese individuals. METHODS: Single-nucleotide polymorphisms (SNP) in the promoter region of the MxA gene were screened, association studies were performed between two SNP and SSPE, and then a functional difference in the promoter activities of the two SNP was investigated by a dual luciferase reporter assay. RESULTS: Four SNP were found ( -88 G/T , -123 C/A , -200 T/C , and -213 G/T ), and SSPE patients exhibited a higher frequency of both the -88T allele and the -88TT genotype than controls (p = 0.040 and 0.003). The IFN-induced up-regulation of the MxA promoter activity of the sequence with -88T was found to be significantly higher than that with G. CONCLUSIONS: MxA promoter -88 G/T SNP may confer host genetic susceptibility to SSPE in Japanese individuals. The finding that homozygotes of the MxA -88T allele with a high MxA -producing capability were more frequently seen in SSPE patients suggests that the MxA protein promotes the establishment of persistent MV infection of neural cells."
],
"offsets": [
[
92,
1423
]
]
}
] | [
{
"id": "f032e12d-f995-4701-9b96-289b4f50275e",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "9f7a30c7-9012-4e38-9992-f093e00f8264",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "7328531f-12cc-402c-8cfd-fd4191077b38",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "8d144ed8-67b4-41b7-b91e-09bb874e9a87",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "93d9ff46-0ed9-4164-be55-0c5988a10622",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "6fac7617-32a7-447c-8ff9-6a8a9c64af4c",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "d888caf1-a036-45f3-a363-f5683b4bdc73",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "bbeb5ade-19f8-475c-95e6-1a0ae4359344",
"type": "gene",
"text": [
"MxA"
],
"offsets": [
[
12,
15
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4599"
}
]
},
{
"id": "e6f1ea94-7f0e-42b7-a8b8-b21ee4ab08c5",
"type": "variant",
"text": [
"-88 G/T"
],
"offsets": [
[
747,
754
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-88T"
}
]
},
{
"id": "e890f573-bb50-4585-8b01-d169a67ebcd6",
"type": "variant",
"text": [
"-123 C/A"
],
"offsets": [
[
758,
766
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-123A"
}
]
},
{
"id": "de7b7aa9-5fff-4f33-b59b-03516265a4a5",
"type": "variant",
"text": [
"-200 T/C"
],
"offsets": [
[
770,
778
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T-200C"
}
]
},
{
"id": "741bfced-64a1-44f3-b7ec-0f9c1af4e35a",
"type": "variant",
"text": [
"-213 G/T"
],
"offsets": [
[
786,
794
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-213T"
}
]
},
{
"id": "4a69c8e0-121c-42c3-85d0-8e43d74a0167",
"type": "variant",
"text": [
"-88 G/T"
],
"offsets": [
[
747,
754
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-88T"
}
]
}
] | [] | [] | [] |
33 | 14961571 | [
{
"id": "e5daca47-e7df-4c8f-8643-90ee6bb04752",
"type": "title",
"text": [
"-160C/A polymorphism in the E-cadherin gene promoter and risk of hereditary, familial and sporadic prostate cancer."
],
"offsets": [
[
0,
118
]
]
},
{
"id": "9666e576-c959-42ac-a172-01f0f2c40ac4",
"type": "abstract",
"text": [
"The E-cadherin (CDH1) gene has been associated with prostate carcinogenesis. The C/A polymorphism--160 base pairs relative to the transcription start site has been shown to decrease gene transcription. We analyzed the association between this polymorphism and the risk of sporadic, familial (2 close relatives) and hereditary (3 or more close relatives) prostate cancer. We combined data from 3 population-based epidemiologic studies in Sweden encompassing altogether 1,036 prostate cancer cases and 669 controls that were genotyped for the short nucleotide polymorphism. Odds ratios with 95% confidence intervals were estimated through unconditional logistic regression. We found no significant association between the A-allele and sporadic (OR = 1.0; 95% CI = 0.8-1.2) or familial (OR = 1.4; 95% CI = 0.9-2.2) prostate cancer. In contrast, risk of hereditary cancer was increased among heterozygote CA carriers (OR = 1.7; 95% CI = 1.0-2.7) and particularly among homozygote AA carriers (OR = 2.6; 95% CI = 1.4-4.9). Our data indicate that the -160 single nucleotide polymorphism in CDH1 is a low-penetrant prostate cancer susceptibility gene that might explain a proportion of familial and notably hereditary prostate cancer."
],
"offsets": [
[
119,
1350
]
]
}
] | [
{
"id": "7c8925dd-a0d1-4650-9086-3c91b6b08f47",
"type": "gene",
"text": [
"E-cadherin"
],
"offsets": [
[
30,
40
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "999"
}
]
},
{
"id": "11a32dcf-650a-44fc-a4c3-856f6b2e0d7a",
"type": "variant",
"text": [
"C/A polymorphism--160 base pairs relative to the transcription start site"
],
"offsets": [
[
203,
276
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-160A"
}
]
}
] | [] | [] | [] |
34 | 14961572 | [
{
"id": "29b88d37-ade0-4b72-ac71-be3459c495ac",
"type": "title",
"text": [
"Polymorphisms of the interleukin-1 beta gene are associated with increased risk of non-small cell lung cancer."
],
"offsets": [
[
0,
112
]
]
},
{
"id": "a7d6a9a3-a57f-48a9-adbe-d7bcb029dac4",
"type": "abstract",
"text": [
"Lung cancer is one of the leading causes of cancer death worldwide. Tobacco smoking is the main risk factor for lung cancer. Less than 20% of smokers develop lung cancer in their lifetime, however, indicating individual variations in lung cancer risk. Pro-inflammatory cytokines produced by inflammatory cells have been associated with inflammatory diseases and cancer. The IL1B gene, encoding IL-1beta cytokine, contains several single nucleotide polymorphisms (SNPs). Two of these are in the promoter region, at positions -511 (C-T) and -31 (T-C) . These polymorphisms have been associated with increased risk of developing a number of inflammatory diseases and gastric carcinoma. We genotyped the 2 polymorphisms in 251 non-small cell lung cancer patients from Norway and 272 healthy controls chosen from the general Norwegian population. The T allele at the -31 SNP (p = 0.01) and C allele at -511 SNP (p < 0.01) were over represented in lung cancer cases. The homozygote subjects were particularly at higher risk of lung cancer with odds ratio of 2.39 (95% CI = 1.29-4.44) for -31T/T and 2.51 (95% CI = 1.47-4.58) for -511C/C genotypes. In view of the significance of the p53 gene in lung carcinogenesis, we also analyzed the IL1B genotypes in relation to p53 mutations in the tumors. The results indicated that subjects having homozygote genotypes were more likely to have a mutation in the p53 gene (p = 0.05). This is the first study to provide evidence for an association of 1L1B gene polymorphisms with lung cancer risk."
],
"offsets": [
[
113,
1666
]
]
}
] | [
{
"id": "e993f6cc-ebae-4329-a8d4-3ae0f376ab48",
"type": "gene",
"text": [
"IL1B"
],
"offsets": [
[
488,
492
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3553"
}
]
},
{
"id": "d91fb3a5-952f-46a3-86b2-1524fa117b31",
"type": "gene",
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"IL-1beta"
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510,
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"db_id": "3553"
}
]
},
{
"id": "85de2741-d117-41c4-b4cf-9f987166a85f",
"type": "gene",
"text": [
"p53"
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1306,
1309
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"db_id": "7157"
}
]
},
{
"id": "ee26b33d-6b47-4add-bd80-777cacdfd89c",
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"IL1B"
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488,
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]
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{
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"p53"
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]
},
{
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"p53"
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1306,
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]
},
{
"id": "b2c71c3f-4e6f-4702-84e5-1d7c4619f7a9",
"type": "variant",
"text": [
"-511 (C-T)"
],
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[
642,
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]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-511T"
}
]
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{
"id": "75608be8-47cc-4478-a4ad-84e2e0022e87",
"type": "variant",
"text": [
"-31 (T-C)"
],
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[
659,
668
]
],
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{
"db_name": "dbSNP",
"db_id": "1143627"
}
]
},
{
"id": "74cc3652-5d33-4f4a-aa6c-db482b0d764c",
"type": "variant",
"text": [
"T allele at the -31 SNP"
],
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[
967,
990
]
],
"normalized": [
{
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"db_id": "1143627"
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]
},
{
"id": "6e31805f-95ca-4a53-99a7-84dea1ac2f0b",
"type": "variant",
"text": [
"C allele at -511 SNP"
],
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[
1008,
1028
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-511C"
}
]
},
{
"id": "bdb59a71-2136-4916-b171-afaddef28039",
"type": "variant",
"text": [
"-31T/T"
],
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1207,
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]
],
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"db_id": "1143627"
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]
},
{
"id": "4bb11f7e-f155-44c7-8468-72c2291dfade",
"type": "variant",
"text": [
"-511C/C"
],
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1250,
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]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-511C"
}
]
}
] | [] | [] | [] |
35 | 14962090 | [
{
"id": "2f81e8b5-7a81-45cf-af8a-c86e64559192",
"type": "title",
"text": [
"Evaluation of the IRF-2 gene as a candidate for PSORS3 ."
],
"offsets": [
[
0,
59
]
]
},
{
"id": "b650eebb-c339-404b-bb72-caec3b3efdca",
"type": "abstract",
"text": [
"Type 1 interferon can trigger flares of psoriasis. Hypersensitivity to type 1 interferon signaling causes a psoriasis-like skin disease in mice deficient for the transcription factor interferon regulatory factor 2 (IRF2). The human IRF2 gene is located at a previously identified candidate psoriasis susceptibility locus on chromosome 4q ( PSORS3 at D4S1535). Therefore, we tested association of psoriasis with IRF2. We generated a sample consisting of 157 families with a total of 521 individuals. Five novel microsatellite markers were developed and typed, and complemented with three known markers to yield a set of eight markers spaced within 600 kb around the IRF2 gene, three of which are located in the gene. We detected association of IRF2 with type 1 psoriasis at two markers in the IRF2 gene. Haplotype sharing analysis confirmed association of IRF2 with type 1 psoriasis (p=0.0017; pcorr=0.03). The 921G/A SNP in exon 9 was found to obliterate a predicted exon splice enhancer in an allele-specific manner. There was a suggestive increase of homozygosity for the splicing-deficient allele in type 1 psoriasis patients. Our data identify IRF2 as a potential susceptibility gene for psoriasis."
],
"offsets": [
[
60,
1265
]
]
}
] | [
{
"id": "0f3b7642-de09-4db1-8bac-dca4f470721d",
"type": "gene",
"text": [
"PSORS3"
],
"offsets": [
[
51,
57
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7889"
}
]
},
{
"id": "4cd3cb31-d04f-48c8-ad45-5d28aaa80498",
"type": "variant",
"text": [
"921G/A "
],
"offsets": [
[
972,
979
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G921A"
}
]
}
] | [] | [] | [] |
36 | 14962947 | [
{
"id": "e55ad154-2de0-4942-a346-b37492cfbde6",
"type": "title",
"text": [
"In-depth haplotype analysis of ABCA1 gene polymorphisms in relation to plasma ApoA1 levels and myocardial infarction."
],
"offsets": [
[
0,
121
]
]
},
{
"id": "42f5a3a9-5d68-4aa4-b313-7f8714e08415",
"type": "abstract",
"text": [
"OBJECTIVE: By regulating the cellular cholesterol efflux from peripheral cells to high-density lipoprotein, the ABCA1 protein is suspected to play a key role in lipid homeostasis and atherosclerosis. Twenty-six polymorphisms of the ABCA1 gene were genotyped and tested for association with plasma levels of ApoA1 and myocardial infarction (MI) in the ECTIM study. METHODS AND RESULTS: In addition to single-locus analysis, a systematic exploration of all possible haplotype effects was performed, with this exploration being performed on a minimal set of \"tag\" polymorphisms that define the haplotype structure of the gene. Two polymorphisms were associated with plasma levels of ApoA1 , 1 in the promoter ( C-564T ) and 1 in the coding ( R1587K ) regions, whereas only 1 polymorphism ( R219K ) was associated with the risk of MI. However, no haplotype effect was detected on ApoA1 variability or on the risk of MI. CONCLUSIONS: ABCA1 gene polymorphisms but not haplotypes are involved in the variability of plasma ApoA1 and the susceptibility to coronary artery disease."
],
"offsets": [
[
122,
1206
]
]
}
] | [
{
"id": "8407fa01-c4a9-490c-91c1-483fa91b757f",
"type": "gene",
"text": [
"ABCA1"
],
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[
32,
37
]
],
"normalized": [
{
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"db_id": "19"
}
]
},
{
"id": "b46306c4-8a09-4965-b2b0-6b42341c588c",
"type": "gene",
"text": [
"ABCA1"
],
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32,
37
]
],
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}
]
},
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"id": "34a8e66f-7d33-4916-a413-da582652111d",
"type": "gene",
"text": [
"ApoA1"
],
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81,
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]
],
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"db_id": "335"
}
]
},
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"id": "3120cb13-51c6-4847-89a0-a78cd7791cb3",
"type": "gene",
"text": [
"ApoA1"
],
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81,
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]
],
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}
]
},
{
"id": "3f933ae3-f459-4b8c-949d-a91d4b03b136",
"type": "gene",
"text": [
"ApoA1"
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81,
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],
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]
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"id": "6f649411-e0a6-4e69-b421-759ece234fc8",
"type": "gene",
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"ABCA1"
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32,
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]
],
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"db_id": "19"
}
]
},
{
"id": "32674c48-e6fd-4bbb-834c-1ff21b8525da",
"type": "gene",
"text": [
"ApoA1"
],
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81,
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]
],
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"db_id": "335"
}
]
},
{
"id": "c542a7d0-d8b1-447c-9c82-99d7fc848ef4",
"type": "variant",
"text": [
"C-564T"
],
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[
837,
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]
],
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{
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"db_id": "C-564T"
}
]
},
{
"id": "6048ac19-634a-4c42-9068-e50fa3b3faf1",
"type": "variant",
"text": [
"R1587K"
],
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[
868,
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]
],
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{
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"db_id": "2230808"
}
]
},
{
"id": "15727abc-e819-45b8-a0ed-6dc645d8e04c",
"type": "variant",
"text": [
"R219K"
],
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[
916,
921
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2230806"
}
]
}
] | [] | [] | [] |
37 | 14970360 | [
{
"id": "11deea42-5057-47d5-b026-eb8baa9ddd54",
"type": "title",
"text": [
"Three single-nucleotide polymorphisms of the angiotensinogen gene and susceptibility to hypertension: single locus genotype vs. haplotype analysis."
],
"offsets": [
[
0,
149
]
]
},
{
"id": "08795029-000e-4a1b-9f68-c5bc19af0e1c",
"type": "abstract",
"text": [
"Although some single polymorphism analyses of the angiotensinogen ( AGT ) gene have been found to be associated with hypertension, the results are still inconsistent. The objectives of this study are to evaluate the association of the genotype and haplotype distributions of three single-nucleotide polymorphisms (SNPs) ( G-217A , A-6G , and M235T ) in the AGT gene with hypertension. In a sample of 461 hypertensive and 327 normotensive patients in Taiwan, we found that -217AA and -6GG homozygotes conferred independently an increased risk to hypertension (P = 0.008 and P = 0.037, respectively), as illustrated by their significant associations with hypertension in both single SNP and pair-wise SNPs analyses. Meanwhile, a very weak linkage disequilibrium was found between the G-217A and the A-6G polymorphisms in terms of r2 (<0.05). On the basis of likelihood ratio test, only the set of haplotypes that constituted the A-6G and the M235T polymorphisms was associated with hypertension (chi2 = 20.91, P = 0.0008), which was mainly due to the increased frequency of the recombinant haplotypes ( -6A identical with 235M and -6G identical with 235T), and a pathophysiological role in the predisposition to hypertension was hence indicated. In functional assays, the promoter activities of the haplotypes -217A identical with -6A and -217G identical with -6G were significantly higher than the most common haplotype -217G identical with -6A . These results highlight the necessity of a thorough analysis of all reported variants of a candidate gene in the elucidation of genetic susceptibility to a complex disease like hypertension, even when the variants are in the same haplotype block."
],
"offsets": [
[
150,
1874
]
]
}
] | [
{
"id": "a8fb5dcc-3c11-4b16-ab49-6515d95fde0c",
"type": "gene",
"text": [
"angiotensinogen"
],
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[
46,
61
]
],
"normalized": [
{
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"db_id": "183"
}
]
},
{
"id": "1d4ec668-d9e4-4d05-966c-8d29aa5e7057",
"type": "gene",
"text": [
"AGT"
],
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[
220,
223
]
],
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}
]
},
{
"id": "5b925983-e8b4-421e-83a5-887c8d06d4eb",
"type": "gene",
"text": [
"AGT"
],
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220,
223
]
],
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}
]
},
{
"id": "c87149e6-1438-4fb9-816a-7988b399d4ff",
"type": "variant",
"text": [
"G-217A"
],
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474,
480
]
],
"normalized": [
{
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"db_id": "G-217A"
}
]
},
{
"id": "4566dd17-2a4a-4f50-a7cc-22fca19de4bb",
"type": "variant",
"text": [
"A-6G"
],
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[
484,
488
]
],
"normalized": [
{
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"db_id": "A-6G"
}
]
},
{
"id": "4b49c284-a4ce-4444-91d3-217f205e5a13",
"type": "variant",
"text": [
"M235T"
],
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496,
501
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "M235T"
}
]
},
{
"id": "7bb89bb5-967b-4d04-980f-7e21f40a4c42",
"type": "variant",
"text": [
"-217AA"
],
"offsets": [
[
629,
635
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "A-217A"
}
]
},
{
"id": "47dcc37e-64a3-4a0d-a298-83111f7156f6",
"type": "variant",
"text": [
"-6GG"
],
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642,
646
]
],
"normalized": [
{
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"db_id": "G-6G"
}
]
},
{
"id": "88f1c7f1-e4d3-459f-905e-88bbdcc80400",
"type": "variant",
"text": [
"G-217A"
],
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474,
480
]
],
"normalized": [
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"db_id": "G-217A"
}
]
},
{
"id": "22e49c89-e010-4693-9450-fa1d9a163786",
"type": "variant",
"text": [
"A-6G"
],
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484,
488
]
],
"normalized": [
{
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"db_id": "A-6G"
}
]
},
{
"id": "d2e43016-7747-4453-b343-db676b47bb24",
"type": "variant",
"text": [
"A-6G"
],
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484,
488
]
],
"normalized": [
{
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"db_id": "A-6G"
}
]
},
{
"id": "0897c50f-a20f-42cb-b06d-9be386ffc5ff",
"type": "variant",
"text": [
"M235T"
],
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496,
501
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "M235T"
}
]
},
{
"id": "9bc4d80f-048d-4db0-954c-4a404f20a7c8",
"type": "variant",
"text": [
"-6A"
],
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[
1269,
1272
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-6A"
}
]
},
{
"id": "064f5cd4-cd13-4351-9967-fbe8f9df04bf",
"type": "variant",
"text": [
"-6G"
],
"offsets": [
[
485,
488
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-6G"
}
]
},
{
"id": "e18d6286-ce08-41ff-aebe-995545b4f8e7",
"type": "variant",
"text": [
"-217A"
],
"offsets": [
[
475,
480
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-217A"
}
]
},
{
"id": "72564ad9-fa82-4880-9454-c5f1be89b19e",
"type": "variant",
"text": [
"-6A"
],
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1269,
1272
]
],
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{
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"db_id": "-6A"
}
]
},
{
"id": "986c7898-a440-4856-84ba-90593ca0a66b",
"type": "variant",
"text": [
"-217G"
],
"offsets": [
[
1513,
1518
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-217G"
}
]
},
{
"id": "5ca1cd8b-7b98-4cab-af60-92bab5d45fea",
"type": "variant",
"text": [
"-6G"
],
"offsets": [
[
485,
488
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-6G"
}
]
},
{
"id": "cec6d24c-78c4-417d-a705-0422d5e2508b",
"type": "variant",
"text": [
"-217G"
],
"offsets": [
[
1513,
1518
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-217G"
}
]
},
{
"id": "932432d6-80e7-4c1a-a244-ced3983df3ac",
"type": "variant",
"text": [
"-6A"
],
"offsets": [
[
1269,
1272
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "-6A"
}
]
}
] | [] | [] | [] |
38 | 14970363 | [
{
"id": "37baa1f1-70df-4026-8b27-7e65235c2007",
"type": "title",
"text": [
"Tests of linkage and/or association of the LEPR gene polymorphisms with obesity phenotypes in Caucasian nuclear families."
],
"offsets": [
[
0,
123
]
]
},
{
"id": "ca9b2d85-4da9-40ba-90c6-4cc63de07efa",
"type": "abstract",
"text": [
"Genetic variations in the leptin receptor ( LEPR ) gene have been conceived to affect body weight in general populations. In this study, using the tests implemented in the statistical package QTDT, we evaluated association and/or linkage of the LEPR gene with obesity phenotypes in a large sample comprising 1,873 subjects from 405 Caucasian nuclear families. Obesity phenotypes tested include body mass index (BMI), fat mass, percentage fat mass (PFM), and lean mass, with the latter three measured by dual-energy X-ray absorptiometry (DXA). Three single nucleotide polymorphisms (SNPs), namely Lys109Arg (A/G) , Lys656Asn (G/C) , Pro1019Pro (G/A) , in the LEPR gene were analyzed. Significant linkage disequilibrium (0.394 < or = |D'| < or = 0.688, P < 0.001) was observed between pairs of the three SNPs. No significant population stratification was found for any SNP/phenotype. In single-locus analyses, evidence of association was observed for Lys656Asn with lean mass (P = 0.002) and fat mass (P = 0.015). The contribution of this polymorphism to the phenotypic variation of lean mass and fat mass was 2.63% and 1.15%, respectively. Subjects carrying allele G at the Lys656Asn site had, on average, 3.16% higher lean mass and 2.71% higher fat mass than those without it. In the analyses for haplotypes defined by the three SNPs, significant associations were detected between haplotype GCA (P = 0.005) and lean mass. In addition, marginally significant evidence of association was observed for this haplotype with fat mass (P = 0.012). No statistically significant linkage was found, largely due to the limited power of the linkage approach to detect small genetic effects in our data sets. Our results suggest that the LEPR gene polymorphisms contribute to variation in obesity phenotypes."
],
"offsets": [
[
124,
1935
]
]
}
] | [
{
"id": "4ed6c30a-4a63-45a3-b055-8f73ef698547",
"type": "gene",
"text": [
"leptin receptor"
],
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[
151,
166
]
],
"normalized": [
{
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}
]
},
{
"id": "ef6f835e-347f-4b36-a6f1-7cbe13bbbe8d",
"type": "gene",
"text": [
"LEPR"
],
"offsets": [
[
44,
48
]
],
"normalized": [
{
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"db_id": "3953"
}
]
},
{
"id": "0161619f-1f8d-4651-b90d-225f473f47ab",
"type": "gene",
"text": [
"LEPR"
],
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[
44,
48
]
],
"normalized": [
{
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"db_id": "3953"
}
]
},
{
"id": "01416876-0b69-41c6-8b43-d27f07ba189d",
"type": "gene",
"text": [
"LEPR"
],
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[
44,
48
]
],
"normalized": [
{
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}
]
},
{
"id": "5a3978af-b5d4-4bff-ae0a-26ec86cf1e53",
"type": "gene",
"text": [
"LEPR"
],
"offsets": [
[
44,
48
]
],
"normalized": [
{
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"db_id": "3953"
}
]
},
{
"id": "a82a9df9-c538-4a47-8036-861d446532e9",
"type": "variant",
"text": [
"Lys109Arg (A/G)"
],
"offsets": [
[
725,
740
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "1137100"
}
]
},
{
"id": "3a9af473-b582-4736-9697-84feaa3ef0fa",
"type": "variant",
"text": [
"Lys656Asn (G/C)"
],
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[
744,
759
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "8179183"
}
]
},
{
"id": "01df9e1c-5e71-435f-8bd2-f9984cb411ce",
"type": "variant",
"text": [
"Pro1019Pro (G/A)"
],
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[
763,
779
]
],
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}
]
},
{
"id": "61dafa2c-7b04-4f4f-823f-8ba15001895d",
"type": "variant",
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"Lys656Asn"
],
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]
],
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}
]
},
{
"id": "ff669c7a-e021-49d8-a031-e17098ad3540",
"type": "variant",
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"Lys656Asn"
],
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744,
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]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "8179183"
}
]
}
] | [] | [] | [] |
39 | 14970845 | [
{
"id": "5e624c83-2f60-4c71-8ac1-d8fabaafde3e",
"type": "title",
"text": [
"Polymorphisms in the prion protein gene and in the doppel gene increase susceptibility for Creutzfeldt-Jakob disease."
],
"offsets": [
[
0,
121
]
]
},
{
"id": "e1ba8a65-52ee-4ca2-876c-c43e8ac8134d",
"type": "abstract",
"text": [
"The prion protein gene ( PRNP ) plays a central role in the origin of Creutzfeldt-Jakob disease (CJD), but there is growing interest in other polymorphisms that may be involved in CJD. Polymorphisms upstream of PRNP that may modulate the prion protein production as well as polymorphisms in the prion-like doppel gene ( PRND ) have been studied, with inconsistent findings. We investigated the role of a single-nucleotide polymorphism ( SNP 1368 ) located upstream of PRNP and three polymorphisms in PRND ( T26M , P56L and T174M ) in CJD. The study included a population-based sample of 52 patients with sporadic CJD and 250 controls. We analysed our data as single markers and haplotypes. Further, we conducted a meta-analysis on PRND T174M comparing the data of the four studies conducted to date. For SNP 1368 and PRNP M129V , we found significant evidence for linkage disequilibrium. No evidence was found for a relation of SNP 1368 to CJD independent of PRNP M129V . We further found a significant increased prevalence of M homozygotes at PRND T174M among sporadic CJD patients, when adjusting the analyses for the other genotypes. In the haplotype analyses, the association was strongest for persons homozygous for PRNP 129M and PRND 174M (odds ratio 4.35, 95% confidence interval 1.05-8.09; P=0.04). The meta-analysis on the PRND T174M polymorphism did not show a consistent effect across studies, raising the question as to whether PRND 174M is causally related to CJD, or whether the PRND allele is in linkage disequilibrium with another polymorphism related to CJD."
],
"offsets": [
[
122,
1748
]
]
}
] | [
{
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"prion protein gene"
],
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22,
40
]
],
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}
]
},
{
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"PRNP"
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149,
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]
},
{
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"PRNP"
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149,
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]
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"prion protein"
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22,
35
]
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}
]
},
{
"id": "2afba729-d85f-44bc-8627-6218c398bcf9",
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"prion-like doppel gene"
],
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424,
446
]
],
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"db_id": "23627"
}
]
},
{
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"PRND"
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450,
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]
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}
]
},
{
"id": "a14ee03c-2065-4cce-b399-598fdec556bc",
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"PRNP"
],
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149,
153
]
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}
]
},
{
"id": "ed9f3b32-14d3-41f5-9bc4-c5003a55fd4a",
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"PRND"
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450,
454
]
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}
]
},
{
"id": "2f3b5003-e6aa-47af-abc2-243320c56d29",
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"PRND"
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450,
454
]
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}
]
},
{
"id": "d1dcba35-634d-4e88-a643-72836be38695",
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"PRNP"
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149,
153
]
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]
},
{
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149,
153
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}
]
},
{
"id": "30b425bf-3390-47fc-be2c-70dfc5050c7a",
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450,
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]
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{
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149,
153
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}
]
},
{
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450,
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},
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"id": "92bff42e-2af2-492b-8859-673032cfad37",
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450,
454
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]
},
{
"id": "dd42e7df-2d4e-4f81-98d9-185f1db90b7a",
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"PRND"
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450,
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]
},
{
"id": "013365a2-92f7-48ce-81bf-fbe56edd60d2",
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"PRND"
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450,
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}
]
},
{
"id": "15f203f0-b207-4833-a407-856427c84cf7",
"type": "variant",
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"SNP 1368"
],
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567,
575
]
],
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}
]
},
{
"id": "4d021d0d-14ff-4476-83cd-4efd897ded77",
"type": "variant",
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"T26M"
],
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641,
645
]
],
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"db_id": "T26M"
}
]
},
{
"id": "79dffd15-ef5d-4265-810c-c940099ef778",
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"P56L"
],
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649,
653
]
],
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}
]
},
{
"id": "b14507b9-58dd-4c94-a56d-27aafd053033",
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"T174M"
],
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660,
665
]
],
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}
]
},
{
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"type": "variant",
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"T174M"
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660,
665
]
],
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}
]
},
{
"id": "02e61bc3-ca33-4f50-a77e-072a8199a8e2",
"type": "variant",
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"SNP 1368"
],
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567,
575
]
],
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}
]
},
{
"id": "b99f0620-9ebd-4ac3-b457-b72b74ace11b",
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"M129V"
],
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968,
973
]
],
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}
]
},
{
"id": "924c7e46-9802-4186-bcd3-b39846d3b9ff",
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567,
575
]
],
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}
]
},
{
"id": "884a0008-81d6-40bc-a092-f19a698f13a8",
"type": "variant",
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"M129V"
],
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968,
973
]
],
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}
]
},
{
"id": "eb2de92d-9448-45f7-8212-de9c298a9546",
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"T174M"
],
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660,
665
]
],
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"db_id": "2245220"
}
]
},
{
"id": "3a4d8011-2810-4905-a1f7-a786cc7b15a2",
"type": "variant",
"text": [
"129M"
],
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[
1384,
1388
]
],
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{
"db_name": "dbSNP",
"db_id": "1799990"
}
]
},
{
"id": "fa0f6958-a125-49a5-9900-7ff1856dfbbd",
"type": "variant",
"text": [
"174M"
],
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[
661,
665
]
],
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"db_id": "2245220"
}
]
},
{
"id": "aa223154-fd60-459b-9948-ff5ba38c3190",
"type": "variant",
"text": [
"T174M"
],
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660,
665
]
],
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"db_id": "2245220"
}
]
},
{
"id": "5974442f-4dd5-4adc-a375-c4cee16dc250",
"type": "variant",
"text": [
"174M"
],
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[
661,
665
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2245220"
}
]
}
] | [] | [] | [] |
40 | 14973548 | [
{
"id": "12d8b008-fae3-4864-9c41-2c895b0a9b9f",
"type": "title",
"text": [
"Is there a future for TNF promoter polymorphisms?"
],
"offsets": [
[
0,
51
]
]
},
{
"id": "bec64891-6f01-4367-80cb-9ac857ddcc8b",
"type": "abstract",
"text": [
"The in vitro study of TNF promoter polymorphism (SNP) function was stimulated by the numerous case-control (association) studies of the polymorphisms in relation to human disease and the appearance of several studies claiming to show a functional role for these SNPs provided a further impetus to researchers interested in the role of TNF in their disease of interest. In this review we consider case-control studies, concentrating on the autoimmune and inflammatory diseases rheumatoid arthritis, multiple sclerosis, ankylosing spondylitis, and asthma, and on infectious diseases including malaria, hepatitis B and C infection, leprosy and sepsis/septic shock. We also review the available evidence on the functional role of the various TNF promoter polymorphisms. In general, case-control studies have produced mixed results, with little consensus in most cases on whether any TNF polymorphisms are actually associated with disease, although results have been more consistent in the case of infectious diseases, particularly malaria. Functional studies have also produced mixed results but recent work suggests that the much studied -308G/A polymorphism is not functional, while the function of other TNF polymorphisms remains controversial. Studies of the TNF region are increasingly using extended haplotypes that can better capture the variation of the MHC region."
],
"offsets": [
[
52,
1435
]
]
}
] | [
{
"id": "4b9f7980-5644-4f59-802e-7683705ed369",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "f1dfb0fc-70d7-493e-be0e-649486dc905f",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
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"db_name": "NCBI Gene",
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}
]
},
{
"id": "8b349363-8c67-4a3a-a022-a4f8789eb7e4",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
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}
]
},
{
"id": "5bf644b6-3ffd-4a4e-9f3f-169c8f31643f",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
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}
]
},
{
"id": "442fc22a-6c9f-4385-87e5-2cc23e850f69",
"type": "gene",
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"TNF"
],
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[
23,
26
]
],
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}
]
},
{
"id": "4c804686-9506-4678-a842-11ac735d9602",
"type": "gene",
"text": [
"TNF"
],
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[
23,
26
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "29463222-1264-4fcd-b12f-4c81ed1c66ec",
"type": "variant",
"text": [
"-308G/A"
],
"offsets": [
[
1196,
1203
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-308A"
}
]
}
] | [] | [] | [] |
41 | 14973783 | [
{
"id": "d25db1e8-e142-4440-9bb8-3ac8bfc48829",
"type": "title",
"text": [
"Melanocortin-4 receptor gene variant I103 is negatively associated with obesity."
],
"offsets": [
[
0,
83
]
]
},
{
"id": "d52006e2-8f4f-41d7-b000-75348fe8f57d",
"type": "abstract",
"text": [
"Several rare mutations in the melanocortin-4 receptor gene (MC4R) predispose to obesity. For the most common missense variant V103I (rs2229616) , however, the previously reported similar carrier frequencies in obese and nonobese individuals are in line with in vitro studies, which have not shown a functional implication of this variant. In the present study, we initially performed a transmission/disequilibrium test on 520 trios with obesity, and we observed a lower transmission rate of the I103 allele (P=.017), which was an unexpected finding. Therefore, we initiated two large case-control studies (N=2,334 and N=661) and combined the data with those from 12 published studies, for a total of 7,713 individuals. The resulting meta-analysis provides evidence for a negative association of the I103 allele with obesity (odds ratio 0.69; 95% confidence interval 0.50-0.96; P=.03), mainly comprising samples of European origin. Additional screening of four other ethnic groups showed comparable I103 carrier frequencies well below 10%. Genomic sequencing of the MC4R gene revealed three polymorphisms in the noncoding region that displayed strong linkage disequilibrium with V103I. In our functional in vitro assays, the variant was indistinguishable from the wild-type allele, as was the result in previous studies. This report on an SNP/haplotype that is negatively associated with obesity expands the successful application of meta-analysis of modest effects in common diseases to a variant with a carrier frequency well below 10%. The respective protective effect against obesity implies that variation in the MC4R gene entails both loss and gain of function."
],
"offsets": [
[
84,
1759
]
]
}
] | [
{
"id": "c9a6c41b-219f-424f-9ab9-fe61fd31c76a",
"type": "gene",
"text": [
"melanocortin-4 receptor gene (MC4R)"
],
"offsets": [
[
115,
150
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4160"
}
]
},
{
"id": "82820722-67fb-4c64-a2e6-90342304d5a3",
"type": "variant",
"text": [
"V103I (rs2229616)"
],
"offsets": [
[
213,
230
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2229616"
}
]
},
{
"id": "05654246-221f-4ce5-b692-85eeb5448c7f",
"type": "variant",
"text": [
"I103"
],
"offsets": [
[
39,
43
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2229616"
}
]
},
{
"id": "19f0ea71-ac52-46d0-9b06-c269bed02709",
"type": "variant",
"text": [
"I103"
],
"offsets": [
[
39,
43
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2229616"
}
]
},
{
"id": "243555a0-fc10-4c2e-9f97-b5a83373abb5",
"type": "variant",
"text": [
"I103"
],
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[
39,
43
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "2229616"
}
]
}
] | [] | [] | [] |
42 | 14975928 | [
{
"id": "b8e83b12-1e5a-4309-9728-a4e75a03bea6",
"type": "title",
"text": [
"Molecular and functional characterization of common polymorphisms in HERG (KCNH2) ) potassium channels."
],
"offsets": [
[
0,
104
]
]
},
{
"id": "d91b6872-f987-4c97-8e64-d03c48f66a11",
"type": "abstract",
"text": [
"Long QT syndrome (LQTS) is a cardiac repolarization disorder that can lead to arrhythmias and sudden death. Chromosome 7-linked inherited LQTS (LQT2) is caused by mutations in human ether-a-go-go-related gene ( HERG ; KCNH2 ), whereas drug-induced LQTS is caused primarily by HERG channel block. Many common polymorphisms are functionally silent and have been traditionally regarded as benign and without physiological consequence. However, the identification of common nonsynonymous single nucleotide polymorphisms (nSNPs; i.e., amino-acid coding variants) with functional phenotypes in the SCN5A Na(+) channel and MiRP1 K(+) channel beta-subunit have challenged this viewpoint. In this report, we test the hypothesis that common missense HERG polymorphisms alter channel physiology. Comprehensive mutational analysis of HERG was performed on genomic DNA derived from a population-based cohort of sudden infant death syndrome and two reference allele cohorts derived from 100 African American and 100 Caucasian individuals. Amino acid-encoding variants were considered common polymorphisms if they were present in at least two of the three study cohorts with an allelic frequency >0.5%. Four nSNPs were identified: K897T , P967L , R1047L , and Q1068R . Wild-type (WT) and polymorphic channels were heterologously expressed in human embryonic kidney cells, and biochemical and voltage-clamp techniques were used to characterize their functional properties. All channel types were processed similarly, but several electrophysiological differences were identified: 1) K897T current density was lower than the other polymorphic channels; 2) K897T channels activated at more negative potentials than WT and R1047L ; 3) K897T and Q1068R channels inactivated and recovered from inactivation faster than WT, P967L , and R1047L channels; and 4) K897T channels showed subtle differences compared with WT channels when stimulated with an action potential waveform. In contrast to K897T and Q1068R channels, P967L and R1047L channels were electrophysiologically indistinguishable from WT channels. All HERG channels had similar sensitivity to block by cisapride. Therefore, some HERG polymorphic channels are electrophysiologically different from WT channels."
],
"offsets": [
[
105,
2390
]
]
}
] | [
{
"id": "25dd7fe5-b936-4a98-ab61-cfa6ba0f338d",
"type": "gene",
"text": [
"HERG"
],
"offsets": [
[
70,
74
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3757"
}
]
},
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{
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]
}
] | [] | [] | [] |
43 | 14979495 | [
{
"id": "f8683426-8805-469e-aa9b-9990da521bdc",
"type": "title",
"text": [
"The Arg753GLn polymorphism of the human toll-like receptor 2 gene in tuberculosis disease."
],
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0,
94
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{
"id": "e6b65436-1e48-4e4b-9133-f1eb0a3bb835",
"type": "abstract",
"text": [
"Toll-like receptor 2 (TLR2) TLR2 ), a member of the Toll-like receptor family, plays an important role in recognition of, and subsequent immune response activation against, mycobacteria. The genetic polymorphism of TLR2 ( arginine to glutamine substitution at residue 753 ( Arg753Gln )) has been associated with a negative influence on TLR2 function, which may, in turn, determine the innate host response to mycobacteria. The aim of the present study was to investigate the Arg753Gln single nucleotide polymorphism of the TLR2 gene in tuberculosis (TB) patients compared to healthy controls. A retrospective case/control study was carried out. The Arg753Gln polymorphism of the TLR2 gene was studied in 151 TB patients compared to 116 ethnically and age-matched healthy control subjects. The TLR2 polymorphism (adenine (A) allele) was observed in 17.9 and 7.7% of TB patients and controls, respectively. When the ratios of the three genotypes were compared between the two groups, the AA genotype was found to be more significantly associated with TB. Allele frequencies for guanine (G) and A were found to be 0.95 and 0.05 in the control group and 0.86 and 0.14 in the TB patient group, respectively. The risk of developing TB disease was increased 6.04- and 1.60-fold for carriers of the AA and GA genotypes, respectively. In conclusion, the present data suggest that the arginine to glutamine substitution at residue 753 polymorphism of the Toll-like receptor 2 gene influences the risk of developing tuberculosis."
],
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[
95,
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]
]
}
] | [
{
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]
},
{
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"arginine to glutamine substitution at residue 753"
],
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],
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]
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{
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{
"id": "e61c8182-4af1-46b7-8e9c-96650aed256d",
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"arginine to glutamine substitution at residue 753"
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]
}
] | [] | [] | [] |
44 | 14986114 | [
{
"id": "ff0cef8d-c475-4e96-a012-b88349d15ab8",
"type": "title",
"text": [
"A single nucleotide polymorphism in the MMP-1 promoter is correlated with histological differentiation of gastric cancer."
],
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[
0,
123
]
]
},
{
"id": "f91062e5-2373-40fb-9d18-1beb52e42747",
"type": "abstract",
"text": [
"PURPOSE: Matrix metalloproteinase-1 ( MMP-1 ) plays a key role in cancer invasion and metastasis by degradation of extracellular matrix (ECM) and basement membrane barriers. The 1G/2G single nucleotide polymorphism (SNP) in the MMP-1 promoter at position -1607 bp has been reported to affect the transcriptional activity. In the light of these findings, we investigated whether this SNP in the MMP-1 promoter is associated with the development, differentiation, and progression of gastric cancer. METHODS: The 215 gastric cancer patients and 166 controls were used in this study. The SNP of the MMP-1 promoter was analyzed by PCR-RFLP and sequencing. The genotype frequency was compared between cases and controls, and the association with clinicopathological parameters among cases was studied. RESULTS: The frequency of 1G/2G genotypes in gastric cancer patients was similar to those in controls (p=0.57). The degree of tumor invasion, the presence of lymph node metastasis, and clinical stage showed no significant association with the SNP. On the other hand, we found a significant association with histological differentiation and gender among gastric cancer patients (p<0.05, respectively). CONCLUSIONS: The presence of 2G allele in the MMP-1 promoter did not enhance the risk of gastric cancer; however, it may be involved in differentiation of gastric cancer."
],
"offsets": [
[
124,
1501
]
]
}
] | [
{
"id": "8b52b6d3-b863-4b86-a4ec-19717d63fa8d",
"type": "gene",
"text": [
"Matrix metalloproteinase-1"
],
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134,
160
]
],
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"db_id": "4312"
}
]
},
{
"id": "af7bc839-ffa6-4cf6-a231-851e3713ca94",
"type": "gene",
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41,
46
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],
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]
},
{
"id": "316b61b0-e792-41e0-b553-2e4f57885dba",
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"MMP-1"
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41,
46
]
],
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]
},
{
"id": "1bc775dc-f7c2-4873-9746-4ba5c8982e2f",
"type": "gene",
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"MMP-1"
],
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41,
46
]
],
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]
},
{
"id": "8e5d56b5-7cdd-404d-b61e-559cc22e8d44",
"type": "gene",
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"MMP-1"
],
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41,
46
]
],
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}
]
},
{
"id": "2ffbb9c0-64ba-40e4-a794-feb3e145e8b7",
"type": "variant",
"text": [
"1G/2G single nucleotide polymorphism (SNP) in the MMP-1 promoter at position -1607 bp"
],
"offsets": [
[
305,
390
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "null"
}
]
}
] | [] | [] | [] |
45 | 14986169 | [
{
"id": "3d16e7b5-139f-47c6-a620-7ff60c1bb06e",
"type": "title",
"text": [
"Association of the T-cell regulatory gene CTLA4 with Graves' disease and autoimmune thyroid disease in the Japanese."
],
"offsets": [
[
0,
118
]
]
},
{
"id": "aab3d27b-502a-476c-a424-42554c09f768",
"type": "abstract",
"text": [
"Autoimmune thyroid disease (AITD) is caused by an immune response to self-thyroid antigen. The cytotoxic T-lymphocyte antigen-4 ( CTLA4 ) gene, encoding a negative regulator of the T-lymphocyte immune response, had been reported to be associated and/or linked to AITD. Recently, AITD susceptibility in the Caucasians was mapped to the 6.1-kb 3'UTR of the CTLA4 gene, in which the three single-nucleotide polymorphisms (SNPs) CT60 , JO31 , and JO30 were strongly associated with AITD. In order to determine the association of the CTLA4 gene with AITD in the Japanese, case-control association analysis for the four SNPs of the CTLA4 gene using 380 AITD patients and 266 healthy controls was done. Among the SNPs examined, the SNP JO31 was most significantly associated with AITD in the Japanese, whereas the association of the JO30 with AITD was not observed. The frequency of the disease-susceptible G allele of the JO31 of the Japanese control was higher than that of the Caucasians (67.1% vs 50.2%); however, the G allele of the JO31 was associated with Graves' disease (GD) (67.1% vs 76.3%, P=0.0013) and AITD in the Japanese (67.1% vs 74.2%, P=0.0055). Furthermore, the G allele of the JO31 was associated with the increased risk for GD [ P=0.0051, odds ratio (OR)=1.7] and AITD ( P=0.016, OR=1.5) in a dominant model. These results suggested that the CTLA4 gene is involved in the susceptibility for GD and AITD in the Japanese."
],
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[
119,
1577
]
]
}
] | [
{
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"cytotoxic T-lymphocyte antigen-4"
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215,
247
]
],
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{
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43,
48
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43,
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{
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550,
554
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],
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}
]
},
{
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],
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558,
562
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],
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]
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{
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570,
574
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{
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562
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{
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{
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},
{
"id": "77c4a217-9d3e-4b42-94d1-33397ed222a1",
"type": "variant",
"text": [
"JO31"
],
"offsets": [
[
558,
562
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "J31O"
}
]
}
] | [] | [] | [] |
46 | 15007371 | [
{
"id": "6c116e57-9a3c-4832-9595-2064f69c3e1c",
"type": "title",
"text": [
"A functional C-G polymorphism in the CYP7B1 promoter region and its different distribution in Orientals and Caucasians."
],
"offsets": [
[
0,
121
]
]
},
{
"id": "00fe5f1d-fa42-4fae-af11-77f847421698",
"type": "abstract",
"text": [
"Cytochrome P450 (CYP) 7B1 is involved in many metabolic processes including androgen metabolism. Genetic variation in the CYP7B1 gene may play a role in predisposition to prostate cancer. Here, we screened the human CYP7B1 gene for possible polymorphisms. Only one single polymorphism was detected, a C-G change in the promoter -104 base pair from the transcription start site. The allele frequency was investigated in Swedish men and compared to a Korean population, as it is known that the frequency of prostate cancer is low among Orientals. We found that the frequency of the G-allele was 4.04% in Swedes (n=150) but only 0.33% among Koreans (n=153). Computer analysis indicated that the two variants bind with different affinities to a CCAAT-box binding protein. Expression studies with reporter constructs showed significantly higher transcriptional activity of the G variant in Hek293 cells (2.7-fold, P<0.05). In conclusion, we report here for the first time the detection of a single polymorphism in the CYP7B1 gene. This polymorphism is associated with phenotypic differences in an expression system and a widely different allele frequency in two ethnic populations, with great differences in the incidence of prostate cancer."
],
"offsets": [
[
122,
1367
]
]
}
] | [
{
"id": "aed5f1bc-7377-40da-8675-385389843407",
"type": "gene",
"text": [
"Cytochrome P450 (CYP) 7B1"
],
"offsets": [
[
122,
147
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9420"
}
]
},
{
"id": "93ed21e2-52c6-4fca-af00-d094f570d1ba",
"type": "gene",
"text": [
"CYP7B1"
],
"offsets": [
[
38,
44
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9420"
}
]
},
{
"id": "c19c9b75-6132-4716-b402-d5ca2c5a9122",
"type": "gene",
"text": [
"CYP7B1"
],
"offsets": [
[
38,
44
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9420"
}
]
},
{
"id": "fff1b6a1-abb6-46c3-a876-791467ec69cc",
"type": "gene",
"text": [
"CYP7B1"
],
"offsets": [
[
38,
44
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "9420"
}
]
},
{
"id": "447bc1cc-e43d-4a45-a747-5db6110a7de0",
"type": "variant",
"text": [
"C-G change in the promoter -104 base pair"
],
"offsets": [
[
429,
470
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-104G"
}
]
}
] | [] | [] | [] |
47 | 15007729 | [
{
"id": "eb0da0df-edac-4e4e-995e-f8d46c640f09",
"type": "title",
"text": [
"Fine mapping of the 2p11 dyslexia locus and exclusion of TACR1 as a candidate gene."
],
"offsets": [
[
0,
85
]
]
},
{
"id": "f72f0e84-492b-4f35-9eb5-bad0e55ef190",
"type": "abstract",
"text": [
"Developmental dyslexia, or reading disability, is a multigenic complex disease for which at least five loci, i.e. DYX1-3 and DYX5-6, have been clearly identified from the human genome. To date, DYX1C1 is the only dyslexia candidate gene cloned. We have previously reported linkage to 2p11 and 7q32 in 11 Finnish pedigrees. Here, we report the fine mapping of the approximately 40-cM linked region from chromosome 2 as we increased marker density to one per 1.8 cM. Linkage was supported with the highest NPL score of 3.0 (P=0.001) for marker D2S2216. Association analysis using the six pedigrees showing linkage pointed to marker D2S286/rs3220265 (P value <0.001) in the near vicinity of D2S2216. We went on to further characterise this approximately 15-cM candidate region (D2S2110-D2S2181) by adding six SNPs covering approximately 670 kb centred at D2S286/rs3220265 . A haplotype pattern could no longer be observed in this region, which was therefore excluded from the candidate area. This also excluded the TACR1 (tachykinin receptor 1) gene, located at marker D2S286. The dyslexia candidate region on 2p11 is, therefore, now limited to the chromosomal area D2S2116-D2S2181, which is approximately 12 Mbp of human sequence and is at a distinct location from the previously reported DYX3 locus, raising the possibility of two distinct loci on chromosome 2p."
],
"offsets": [
[
86,
1456
]
]
}
] | [
{
"id": "296ed6b2-1396-4ba7-9b86-99d08c404c83",
"type": "gene",
"text": [
"DYX1C1"
],
"offsets": [
[
281,
287
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "161582"
}
]
},
{
"id": "c155db4d-b23c-4512-b663-2a0c9e9d3710",
"type": "gene",
"text": [
"TACR1"
],
"offsets": [
[
58,
63
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "6869"
}
]
},
{
"id": "b6f55756-c926-499a-93c2-1f7c8e6cc165",
"type": "gene",
"text": [
"DYX3"
],
"offsets": [
[
1381,
1385
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "11192"
}
]
},
{
"id": "08a120a9-947c-48af-b6d0-ab70585e16a1",
"type": "variant",
"text": [
"D2S286/rs3220265"
],
"offsets": [
[
719,
735
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3220265"
}
]
},
{
"id": "be4907be-6954-4cd1-b355-5ee0443a37f0",
"type": "variant",
"text": [
"D2S286/rs3220265"
],
"offsets": [
[
719,
735
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "3220265"
}
]
}
] | [] | [] | [] |
48 | 15008790 | [
{
"id": "a671c667-10ec-4931-9fa2-15774e222cfe",
"type": "title",
"text": [
"Population differences in DNA sequence variation and linkage disequilibrium at the PON1 gene."
],
"offsets": [
[
0,
95
]
]
},
{
"id": "bda16d5d-992f-4a63-aeee-b87eebbd5d26",
"type": "abstract",
"text": [
"Polymorphisms of the promoter region (-108C/T) and the coding region (192Q/R) of the paraoxonase 1 gene ( PON1 ) showed differences in association with cardiovascular disease risk in various populations. To characterize the genetic variation underlying these important polymorphisms, we examined DNA sequence variation both in a 1.3-kb promoter region 16.5 kb from codon 192, and in a 1.7-kb region centered on the 192Q/R polymorphic site of the coding region of PON1 , in 30 Africans, 30 Europeans and 64 Japanese. We found 10 polymorphic sites and 11 haplotypes in the 1.3-kb promoter region and 10 biallelic polymorphic sites and 10 haplotypes in the 1.7-kb region. From the PON1 sequences of chimpanzees and an orangutan, the ancestral type of codon 192 was found to be R. The number of pairs of polymorphic sites between the promoter and 1.7-kb regions that were in significant linkage disequilibrium was much higher in a Japanese population than in African and European populations. In addition, the pairs of polymorphic sites in linkage disequilibrium differed among the three populations. These results suggest that some of the population differences in association with risk for coronary heart disease can be explained by population differences in haplotype frequency of PON1 haplotypes."
],
"offsets": [
[
96,
1403
]
]
}
] | [
{
"id": "321a2115-09f6-4755-9600-33f16acb1976",
"type": "gene",
"text": [
"paraoxonase 1 gene"
],
"offsets": [
[
186,
204
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "2754341f-812b-452e-bed8-644b650c3706",
"type": "gene",
"text": [
"PON1"
],
"offsets": [
[
84,
88
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "bd0df2a5-9d11-4b00-93d7-a4ea0a0b1553",
"type": "gene",
"text": [
"PON1"
],
"offsets": [
[
84,
88
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "9c0ffb24-f979-4385-b31d-97225ee7b055",
"type": "gene",
"text": [
"PON1"
],
"offsets": [
[
84,
88
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "4cf8c9fd-b7fd-4b4a-b2d4-f0e9d1cf545c",
"type": "gene",
"text": [
"PON1"
],
"offsets": [
[
84,
88
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5444"
}
]
},
{
"id": "f214d583-5b3d-412e-af8c-f57df16de694",
"type": "variant",
"text": [
"(-108C/T)"
],
"offsets": [
[
134,
143
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-108T"
}
]
},
{
"id": "64ada24b-c9c0-4597-be7e-11d2a2601e0b",
"type": "variant",
"text": [
"(192Q/R)"
],
"offsets": [
[
168,
176
]
],
"normalized": [
{
"db_name": "dbSNP",
"db_id": "662"
}
]
}
] | [] | [] | [] |
49 | 15009068 | [
{
"id": "3e2ae00d-8b54-4b23-8da0-a9bf942eeaf0",
"type": "title",
"text": [
"Single nucleotide polymorphisms of the inflammatory cytokine genes in adults with chronic immune thrombocytopenic purpura."
],
"offsets": [
[
0,
122
]
]
},
{
"id": "601e8809-4702-408e-918a-a5dee4430dde",
"type": "abstract",
"text": [
"Single nucleotide polymorphisms (SNPs) of inflammatory cytokine genes were examined in 84 adult Japanese patients with chronic immune thrombocytopenic purpura (ITP) and 56 race-matched healthy controls. The SNPs examined were within the genes encoding tumour necrosis factor (TNF)-alpha ( -238 G/A and -308 G/A ), TNF-beta ( +252 G/A ), and interleukin (IL)-1beta ( -511 C/T and +3953 T/C ). Of these SNPs, the frequency of the TNF-beta (+252) G/G phenotype was significantly higher in ITP patients than in healthy controls (21% vs. 7%, P = 0.04, odds ratio = 3.6, 95% confidence interval 1.1-11.1), while no significant association was detected for the other SNPs. The distribution of the TNF-beta (+252) phenotype was not associated with human leucocyte antigen class II alleles or the therapeutic response in ITP patients. The frequency of circulating anti-glycoprotein IIb/IIIa antibody-producing B cells was significantly higher in ITP patients with the TNF-beta (+252) G/G phenotype than in those with the G/A or A/A phenotype (11.9 +/- 4.9 vs. 6.8 +/- 4.9 and 3.7 +/- 2.8 per 10(5) peripheral blood mononuclear cells; P = 0.02 and P < 0.001, respectively). These findings suggest that the SNP located at TNF-beta (+252) contributes to susceptibility to chronic ITP by controlling the autoreactive B-cell responses to platelet membrane glycoproteins."
],
"offsets": [
[
123,
1501
]
]
}
] | [
{
"id": "a7df69f5-f580-46f3-add9-81f965be0276",
"type": "gene",
"text": [
"tumour necrosis factor (TNF)-alpha"
],
"offsets": [
[
376,
410
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "7124"
}
]
},
{
"id": "13c0bd48-554c-4dc6-bfba-c77f521c2b77",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "f88fcc23-bdb3-411e-b5bf-a5b199c85ccf",
"type": "gene",
"text": [
"interleukin (IL)-1beta"
],
"offsets": [
[
471,
493
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "3553"
}
]
},
{
"id": "0c84f3da-a5a6-480d-ba80-2d0aceeeeca9",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "65319a3b-043a-4d54-84f2-7205352131fc",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "01a009d6-ab44-4aac-9b08-928f0bacb6fb",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "7d41f194-3f15-49c7-8455-5aa2725a0311",
"type": "gene",
"text": [
"TNF-beta"
],
"offsets": [
[
442,
450
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "4049"
}
]
},
{
"id": "d7fec9e6-22d6-4e42-aa5d-17777cd9dab1",
"type": "variant",
"text": [
"-238 G/A"
],
"offsets": [
[
414,
422
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-238A"
}
]
},
{
"id": "b0bc1fc2-3856-4d13-9f9d-cc823a58aa91",
"type": "variant",
"text": [
"-308 G/A"
],
"offsets": [
[
429,
437
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G-308A"
}
]
},
{
"id": "44a74954-1256-4520-99bd-fd5382b46089",
"type": "variant",
"text": [
"+252 G/A"
],
"offsets": [
[
454,
462
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G252A"
}
]
},
{
"id": "91eb5aba-473f-4d59-97cc-3cfdf5b01a94",
"type": "variant",
"text": [
"-511 C/T"
],
"offsets": [
[
497,
505
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C-511T"
}
]
},
{
"id": "96b7abaa-175d-445e-9596-ea81ad687fc2",
"type": "variant",
"text": [
"+3953 T/C"
],
"offsets": [
[
512,
521
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "T3953C"
}
]
},
{
"id": "53fb615b-82d8-4273-b5bd-8b3b102012ee",
"type": "variant",
"text": [
"(+252) G/G"
],
"offsets": [
[
573,
583
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G252G"
}
]
},
{
"id": "4d6edf8f-fb01-4d74-9915-8ae7a7034b66",
"type": "variant",
"text": [
"(+252) G/G"
],
"offsets": [
[
573,
583
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "G252G"
}
]
}
] | [] | [] | [] |
50 | 15022318 | [
{
"id": "e27591f3-867c-4920-a81e-2aeebdd203e2",
"type": "title",
"text": [
"Association of a programmed death 1 gene polymorphism with the development of rheumatoid arthritis, but not systemic lupus erythematosus."
],
"offsets": [
[
0,
139
]
]
},
{
"id": "241e9bbc-c433-43bc-adc6-a6aa73784f80",
"type": "abstract",
"text": [
"OBJECTIVE: The expression of autoimmunity in mice deficient in programmed death 1 ( PD-1 ) suggests that PD-1 is a candidate gene involved in the development of human autoimmune diseases such as systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). We therefore tested the potential association between PD-1 and the development of SLE and RA by conducting case-control genetic-association studies. METHODS: Ninety-eight SLE patients, 84 RA patients, and sex-matched control subjects for each disease group were recruited and genotyped for a single-nucleotide polymorphism, C+872T , in the human PD-1 gene. The significance of the association of the PD-1 gene with SLE or with RA was analyzed by statistical tests for the difference in genotype distribution between disease and control groups. RESULTS: The human PD-1 gene was found to be significantly associated with disease development in RA patients, but not SLE patients. The risk of RA development appeared to be significantly increased by carriage of the T allele (odds ratio 3.32, P < 0.0001) or the C/T genotype (odds ratio 3.52, P < 0.00005). CONCLUSION: The PD-1 gene is significantly associated with RA susceptibility, suggesting the possibility that PD-1 may contribute to the pathogenesis of RA."
],
"offsets": [
[
140,
1427
]
]
}
] | [
{
"id": "1d574fe0-5928-40c7-a7b9-082c2c676ca7",
"type": "gene",
"text": [
"programmed death 1"
],
"offsets": [
[
18,
36
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "8af6de55-54e8-4db5-9f9c-ad2ff4de0068",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "987f0507-3a17-46ca-ab4d-b36bad059940",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "71f9722c-53b3-4fee-b4bd-9444f76623a9",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "cf86b358-6031-4299-8f0d-67016060a4a9",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "04348b83-bbfa-4c97-a877-591131749732",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "e659bf38-1d21-4ed6-87f4-7a4a4eb91f48",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "070e1655-7949-4a6b-a838-b6b2490cbdec",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "e7776cf7-a348-4f73-b98a-c6972d78c761",
"type": "gene",
"text": [
"PD-1"
],
"offsets": [
[
226,
230
]
],
"normalized": [
{
"db_name": "NCBI Gene",
"db_id": "5133"
}
]
},
{
"id": "2d44d44d-8f15-46c4-b500-9b3b73a8f722",
"type": "variant",
"text": [
"C+872T"
],
"offsets": [
[
732,
738
]
],
"normalized": [
{
"db_name": "HGVS-like",
"db_id": "C872T"
}
]
}
] | [] | [] | [] |
51 | 15024396 | [
{
"id": "89e6cf82-e158-45db-b937-96dc3c9968a5",
"type": "title",
"text": [
"Association of the homeobox transcription factor, ENGRAILED 2 , 3, with autism spectrum disorder."
],
"offsets": [
[
0,
98
]
]
},
{
"id": "a1195aab-d093-426c-997a-f1cdbcebe38d",
"type": "abstract",
"text": [
"Mouse mutants of the homeobox transcription factor Engrailed2 (En2) and autistic individuals display similar cerebellar morphological abnormalities, which include hypoplasia and a decrease in the number of Purkinje cells. Human EN2 maps to 7q36, a chromosomal region that has demonstrated suggestive linkage to autism spectrum disorder (ASD). To investigate EN2 for evidence of association with ASD, four single-nucleotide polymorphisms (SNPs) ( rs3735653 , rs1861972 , rs1861973 , rs2361689 ) that span the majority of the 8.0 kb gene were assessed by the transmission/disequilibrium test. Initially, 138 triads of autistic individuals and their parents were tested. Two intronic SNPs ( rs1861972 and rs1861973 ) demonstrated significant association with autism ( rs1861972 , P=0.0018; rs1861973 , P=0.0003; haplotype, P=0.000005). Flanking exonic SNPs ( rs3735653 and rs2361689 ) did not display association. This analysis was then extended to include 167 small nuclear ASD pedigrees and significant association was again only observed for rs1861972 and rs1861973 under both the narrow and broad diagnostic criteria (narrow: rs1861972 P=0.0290, rs1861973 P=0.0073, haplotype P=0.0009; broad: rs1861972 P=0.0175, rs1861973 P=0.0107, haplotype P=0.0024). These data demonstrate association between a cerebellar patterning gene and ASD, suggesting a role for EN2 as a susceptibility locus and supporting a neurodevelopmental defect hypothesis in the etiology of autism."
],
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{
"id": "ecda1580-a66d-4ce5-a8cc-82b0cf18cf4c",
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"text": [
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{
"id": "076f6e9c-805a-490b-a4ae-1ebc741dc5a6",
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"normalized": [
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}
]
}
] | [] | [] | [] |
52 | 15024686 | [
{
"id": "7e078deb-9cab-465e-92bf-bfa2e76b913f",
"type": "title",
"text": [
"Crohn disease: frequency and nature of CARD15 mutations in Ashkenazi and Sephardi/Oriental Jewish families."
],
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{
"id": "323a392e-a2f5-4467-acd3-d84c5a62f47e",
"type": "abstract",
"text": [
"Crohn disease (CD), an inflammatory bowel disease, is a multifactorial trait with the highest frequency in Ashkenazi Jewish (AJ) individuals of Central European origin. Recently, three common predisposing CARD15 mutations ( R702W , G908R , and 1007fs ) and a polymorphism ( P268S ) were identified. To determine whether CARD15 mutations account for the higher prevalence of CD in AJ individuals, the haplotypes and allele frequencies of the common mutations and variants were assessed in 219 members of 50 AJ and 53 members of 10 Sephardi/Oriental Jewish (SOJ) multiplex families with CD, in 36 AJ patients with sporadic CD, and in 246 AJ and 82 SOJ controls. A higher frequency of CARD15 mutations was found in AJ patients from multiplex families with CD from Central (44.0%) versus Eastern (24.0%) Europe, especially for G908R and 1007fs , and in SOJ patients (34.5%) compared with AJ (10.1%) or SOJ (5.4%) controls. Contrary to expectation, the frequency of the common mutations was slightly lower in AJ patients with CD (30.1%) than in SOJ patients with CD (34.5%). The 702W allele was associated with both the P268 and 268S alleles. CARD15 mutation frequencies were greater in affected sib pairs than in sporadic CD cases but actually decreased in families with three or more affected sibs, raising the possibility of genetic heterogeneity. Similarly, our linkage evidence on chromosome 16 was diminished in the families with three or more affected sibs compared with sib pairs. Screening the CARD15 gene for rare variants revealed five novel changes (D113N, D357A , I363F , L550V , and N852S ) of which N852S occurred only in AJ individuals and may be disease predisposing. Also, there was no evidence for increased risk associated with the recently described IVS(+158) single-nucleotide polymorphism. Although the AJ controls appear to have a higher frequency of CARD15 mutations than the SOJ controls, it is unlikely that this difference fully explains the excess frequency of CD in the AJ population."
],
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{
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]
},
{
"id": "e9268b97-93d6-48db-973d-1bb99b52b5b9",
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"text": [
"1007fs"
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},
{
"id": "21a616b0-202c-44ce-89a9-b0e84e16f173",
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"text": [
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},
{
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{
"id": "5cc7c5d5-c2f5-4b0b-990b-29e7b16f2245",
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{
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]
}
] | [] | [] | [] |
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Dataset Card for OSIRIS
The OSIRIS corpus is a set of MEDLINE abstracts manually annotated with human variation mentions. The corpus is distributed under the terms of the Creative Commons Attribution License Creative Commons Attribution 3.0 Unported License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (Furlong et al, BMC Bioinformatics 2008, 9:84).
Citation Information
@ARTICLE{Furlong2008,
author = {Laura I Furlong and Holger Dach and Martin Hofmann-Apitius and Ferran Sanz},
title = {OSIRISv1.2: a named entity recognition system for sequence variants
of genes in biomedical literature.},
journal = {BMC Bioinformatics},
year = {2008},
volume = {9},
pages = {84},
doi = {10.1186/1471-2105-9-84},
pii = {1471-2105-9-84},
pmid = {18251998},
timestamp = {2013.01.15},
url = {http://dx.doi.org/10.1186/1471-2105-9-84}
}
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