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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rs6756629

Associations

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: 2 x 10-11
Odds ratio [95% confidence interval]: .15 [NR] s.d. increase
Gene: ABCG5;ABCG8
Risk allele: G
Minor allele frequency (controls): 0.92

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: LDL cholesterol
Study population: 17,797 individuals
Association P-value: 3 x 10-10
Odds ratio [95% confidence interval]: .16 [NR] s.d. increase
Gene: ABCG5;ABCG8
Risk allele: G
Minor allele frequency (controls): 0.92

Lead SNP

rs6756629
Position: chr2:44,065,090 (Open in UCSC Genome Browser)
Distance to nearest TSS: 729 bp
GENCODE v7 location: Coding region
No regulatory annotation found

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 

SNPs in the linkage disequilibrium region sorted by decreasing amount of evidence supporting a functional role for the SNP:

rs4953023
Position: chr2:44,074,000 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,910 bp
Distance to nearest TSS: 31,053 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.867




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 01:19:12
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