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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rs3846662

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: 3 x 10-19
Odds ratio [95% confidence interval]: .09 [NR] s.d. increase
Gene: HMGCR
Risk allele: G
Minor allele frequency (controls): 0.44

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: 2 x 10-11
Odds ratio [95% confidence interval]: .08 [NR] s.d. increase
Gene: HMGCR
Risk allele: G
Minor allele frequency (controls): 0.44

Lead SNP

rs3846662
Position: chr5:74,651,084 (Open in UCSC Genome Browser)
Distance to nearest TSS: 18,344 bp
GENCODE v7 location: Intron
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:

rs4549504
Position: chr5:74,808,237 (Open in UCSC Genome Browser)
Distance to lead SNP: 157,153 bp
Distance to nearest TSS: 26,247 bp
GENCODE v7 location: Exon, non-coding
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=0.909 / JPT: D'=1.0, r2=0.908 / YRI: D'=1.0, r2=1.0

rs4704220
Position: chr5:74,757,556 (Open in UCSC Genome Browser)
Distance to lead SNP: 106,472 bp
Distance to nearest TSS: 75,807 bp
GENCODE v7 location: Intron
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=0.954 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs4604177
Position: chr5:74,808,880 (Open in UCSC Genome Browser)
Distance to lead SNP: 157,796 bp
Distance to nearest TSS: 25,604 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=0.954 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs4704221
Position: chr5:74,759,183 (Open in UCSC Genome Browser)
Distance to lead SNP: 108,099 bp
Distance to nearest TSS: 77,434 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=0.909 / JPT: D'=1.0, r2=0.908 / YRI: D'=1.0, r2=1.0

rs6896136
Position: chr5:74,787,310 (Open in UCSC Genome Browser)
Distance to lead SNP: 136,226 bp
Distance to nearest TSS: 105,561 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=0.954 / JPT: D'=1.0, r2=0.953 / YRI: D'=1.0, r2=1.0

rs4704223
Position: chr5:74,773,420 (Open in UCSC Genome Browser)
Distance to lead SNP: 122,336 bp
Distance to nearest TSS: 91,671 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=0.954 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs6878990
Position: chr5:74,689,249 (Open in UCSC Genome Browser)
Distance to lead SNP: 38,165 bp
Distance to nearest TSS: 117,784 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.924 / CHB: D'=1.0, r2=0.868 / JPT: D'=1.0, r2=0.902 / YRI: D'=1.0, r2=0.866

rs4704219
Position: chr5:74,748,505 (Open in UCSC Genome Browser)
Distance to lead SNP: 97,421 bp
Distance to nearest TSS: 66,756 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.96 / CHB: D'=1.0, r2=0.907 / JPT: D'=1.0, r2=0.908 / YRI: D'=1.0, r2=1.0




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 01:19:15
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