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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rs738322

Associations

Study: Genome-wide association study identifies nidogen 1 (NID1) as a susceptibility locus to cutaneous nevi and melanoma risk. [PMID:21478494]
First author: Nan H
Journal: Hum Mol Genet
Date: 04/09/2011
Phenotype: Cutaneous nevi
Study population: 9,136 European ancestry individuals
Replication population: 3,581 European ancestry individuals
Association P-value: 1 x 10-06
Odds ratio [95% confidence interval]: .06 [0.04-0.08] unit decrease
Gene: PLA2G6
Risk allele: G
Minor allele frequency (controls): 0.46

Lead SNP

rs738322
Position: chr22:38,569,006 (Open in UCSC Genome Browser)
Distance to nearest TSS: 41,880 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:

rs133024
Position: chr22:38,574,066 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,060 bp
Distance to nearest TSS: 36,820 bp
GENCODE v7 location: Intron
RegulomeDB Score: 2b - ChIP-seq peak + any motif + matched DNase Footprint + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.962 / CHB: D'=1.0, r2=1.0 / JPT: D'=0.937, r2=0.784 / YRI: D'=0.857, r2=0.645

rs133016
Position: chr22:38,572,582 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,576 bp
Distance to nearest TSS: 38,304 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.943 / YRI: D'=0.845, r2=0.621

rs133017
Position: chr22:38,572,637 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,631 bp
Distance to nearest TSS: 38,249 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.943 / YRI: D'=0.857, r2=0.645

rs2413503
Position: chr22:38,568,944 (Open in UCSC Genome Browser)
Distance to lead SNP: 62 bp
Distance to nearest TSS: 41,942 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.953, r2=0.83

rs2092180
Position: chr22:38,571,563 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,557 bp
Distance to nearest TSS: 39,323 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.943 / YRI: D'=0.855, r2=0.615

rs84473
Position: chr22:38,557,326 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,680 bp
Distance to nearest TSS: 50,793 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=1.0 / CHB: D'=1.0, r2=0.949 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.865, r2=0.749

rs75387
Position: chr22:38,572,057 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,051 bp
Distance to nearest TSS: 38,829 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.943 / YRI: D'=0.855, r2=0.615

rs133012
Position: chr22:38,570,721 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,715 bp
Distance to nearest TSS: 40,165 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.943 / YRI: D'=0.834, r2=0.573

rs133021
Position: chr22:38,573,338 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,332 bp
Distance to nearest TSS: 37,548 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.943

rs4382
Position: chr22:38,570,842 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,836 bp
Distance to nearest TSS: 40,044 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.943 / YRI: D'=0.851, r2=0.606

rs4385
Position: chr22:38,573,229 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,223 bp
Distance to nearest TSS: 37,657 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.943 / YRI: D'=0.857, r2=0.645

rs132985
Position: chr22:38,563,471 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,535 bp
Distance to nearest TSS: 56,938 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.907, r2=0.754

rs4383
Position: chr22:38,570,927 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,921 bp
Distance to nearest TSS: 39,959 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=0.943 / YRI: D'=0.838, r2=0.582

rs132941
Position: chr22:38,545,942 (Open in UCSC Genome Browser)
Distance to lead SNP: 23,064 bp
Distance to nearest TSS: 39,409 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.918 / CHB: D'=1.0, r2=0.903 / JPT: D'=0.939, r2=0.882




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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