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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rs2284063

Associations

Study: Genome-wide association study identifies three loci associated with melanoma risk. [PMID:19578364]
First author: Bishop DT
Journal: Nat Genet
Date: 07/05/2009
Phenotype: Melanoma
Study population: 1,539 European ancestry cases, 3,917 European ancestry controls
Replication population: 2,312 European ancestry cases, 1,867 European ancestry controls
Association P-value: 2 x 10-09
Odds ratio [95% confidence interval]: 1.20 [1.14-1.28]
Gene: PLA2G6
Minor allele frequency (controls): 0.37

Study: Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi. [PMID:19578365]
First author: Falchi M
Journal: Nat Genet
Date: 07/05/2009
Phenotype: Cutaneous nevi
Study population: 1,524 European twins
Replication population: 4,107 European individuals
Association P-value: 3 x 10-08
Odds ratio [95% confidence interval]: .08 [-0.002-0.16] decrease in log nevus count
Gene: PLA2G6
Risk allele: G
Minor allele frequency (controls): 0.35

Lead SNP

rs2284063
Position: chr22:38,544,298 (Open in UCSC Genome Browser)
Distance to nearest TSS: 37,765 bp
GENCODE v7 location: Intron
RegulomeDB Score: 4 - ChIP-seq peak + 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 

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

rs4821751
Position: chr22:38,564,457 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,159 bp
Distance to nearest TSS: 977 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=0.916 / CHB: D'=1.0, r2=0.931 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.925, r2=0.857

rs6001029
Position: chr22:38,555,193 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,895 bp
Distance to nearest TSS: 48,660 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=0.863 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.924, r2=0.823

rs6001027
Position: chr22:38,545,619 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,321 bp
Distance to nearest TSS: 39,086 bp
GENCODE v7 location: Intron
No regulatory annotation found
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=1.0

rs5756932
Position: chr22:38,546,118 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,820 bp
Distance to nearest TSS: 39,585 bp
GENCODE v7 location: Intron
No regulatory annotation found
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=0.859




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 01:19:25
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