Linking Disease Associations with Regulatory Information in the Human Genome - Companion website
Marc A. Schaub, Alan P. Boyle, Anshul Kundaje, Serafim Batzoglou, Michael Snyder, Stanford University

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rs2075650

Associations

Study: Genome-wide association study of CSF biomarkers Abeta1-42, t-tau, and p-tau181p in the ADNI cohort. [PMID:21123754]
First author: Kim S
Journal: Neurology
Date: 12/01/2010
Phenotype: Alzheimer's disease biomarkers
Study population: 374 non-Hispanic Caucasians
Association P-value: 1 x 10-06
Gene: TOMM40

Study: Genome-wide association reveals genetic effects on human Aβ42 and ? protein levels in cerebrospinal fluids: a case control study. [PMID:20932310]
First author: Han MR
Journal: BMC Neurol
Date: 10/08/2010
Phenotype: AB1-42
Study population: 243 normal, 235 mild cognitive impaired, and 340 Alzheimer's Disease individuals
Association P-value: 3 x 10-07
Gene: TOMM40
Risk allele: G

Study: Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease provides genetic evidence for folate-pathway abnormalities. [PMID:20885792]
First author: Naj AC
Journal: PLoS Genet
Date: 09/23/2010
Phenotype: Alzheimer's disease (late onset)
Study population: 931 cases, 1,104 controls
Replication population: 1,338 cases, 2,003 controls
Association P-value: 5 x 10-36
Odds ratio [95% confidence interval]: 2.94 [2.48-3.47]
Gene: TOMM40
Risk allele: G
Minor allele frequency (controls): 0.20

Study: Genetic signatures of exceptional longevity in humans. [PMID:20595579]
First author: Sebastiani P
Journal: Science
Date: 07/01/2010
Phenotype: Longevity
Study population: 801 Caucasian centenarians, 926 Caucasian controls
Replication population: 254 Caucasian centenarians, 341 Caucasian controls
Association P-value: 8 x 10-12
Odds ratio [95% confidence interval]: 2.08 [NR]
Gene: TOMM40
Risk allele: A
Minor allele frequency (controls): 0.74

Study: Genome-wide analysis of genetic loci associated with Alzheimer disease. [PMID:20460622]
First author: Seshadri S
Journal: JAMA
Date: 05/12/2010
Phenotype: Alzheimer's disease
Study population: 8,935 white individuals with 973 incident cases, 2,033 white prevalent cases, 14,642 white controls
Replication population: 6,505 white cases, 13,532 white controls
Association P-value: 1 x 10-295
Odds ratio [95% confidence interval]: 2.53 [2.41-2.66]
Gene: TOMM40
Risk allele: G
Minor allele frequency (controls): 0.14

Study: Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort. [PMID:20100581]
First author: Shen L
Journal: Neuroimage
Date: 01/22/2010
Phenotype: Brain imaging
Study population: 175 Caucasian Alzheimer patients, 354 Caucasian amnestic mild cognitive impairment patients, 204 Caucasian controls
Association P-value: 1
Gene: -

Study: Genome-Wide Scan of Copy Number Variation in Late-Onset Alzheimer's Disease. [PMID:term=200]
First author: Heinzen EL
Journal: J Alzheimers Dis
Date: 09/11/2009
Phenotype: Alzheimer's disease
Study population: 331 cases, 368 controls
Association P-value: 3 x 10-11
Gene: TOMM40
Minor allele frequency (controls): 0.15

Study: Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. [PMID:19734902]
First author: Harold D
Journal: Nat Genet
Date: 09/06/2009
Phenotype: Alzheimer's disease
Study population: 3,941 European ancestry cases, 7,848 European ancestry controls
Replication population: 2,023 European ancestry cases, 2,340 European ancestry controls
Association P-value: 2 x 10-157
Odds ratio [95% confidence interval]: 2.53 [2.37-2.71]
Gene: TOMM40
Minor allele frequency (controls): 0.15

Study: Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease. [PMID:19734903]
First author: Lambert JC
Journal: Nat Genet
Date: 09/06/2009
Phenotype: Alzheimer's disease
Study population: 2,032 French cases, 5,328 French controls
Replication population: 3,978 European cases, 3,297 European controls
Association P-value: 2 x 10-16
Gene: TOMM40
Minor allele frequency (controls): 0.90

Study: Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. [PMID:19060911]
First author: Aulchenko YS
Journal: Nat Genet
Date: 12/07/2008
Phenotype: Cholesterol, total
Study population: 22,562 individuals
Association P-value: 3 x 10-19
Odds ratio [95% confidence interval]: .14 [NR] s.d. increase
Gene: TOMM40
Risk allele: G
Minor allele frequency (controls): 0.15

Study: Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. [PMID:18439552]
First author: Reiner AP
Journal: Am J Hum Genet
Date: 04/24/2008
Phenotype: C-reactive protein
Study population: 909 individuals
Replication population: 5,106 individuals
Association P-value: 1 x 10-07
Gene: TOMM40

Lead SNP

rs2075650
Position: chr19:45,395,619 (Open in UCSC Genome Browser)
Distance to nearest TSS: 10,808 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)

Linkage disequilibrium region

Linkage disequilibrium threshold:
 - In all HapMap 2 populations: r2≥0.8 r2≥0.9 r2=1.0 
 - In the HapMap 2 CEU population r2≥0.8 r2≥0.9 r2=1.0 

No SNPs found for this LD threshold.




Credits:
This resource uses data from:
 - The NHGRI GWAS catalog (accessed August 10, 2011)
 - The ENCODE project
 - RegulomeDB
 - The HapMap project

Contact: marc.schaub AT cs.stanford.edu
Last modified: 2011-12-15 01:19:24
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