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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rs3768080

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: 7 x 10-08
Odds ratio [95% confidence interval]: .07 [0.05-0.09] unit decrease
Gene: NID1
Risk allele: A
Minor allele frequency (controls): 0.51

Lead SNP

rs3768080
Position: chr1:236,179,869 (Open in UCSC Genome Browser)
Distance to nearest TSS: 44,743 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:

rs2031487
Position: chr1:236,175,339 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,530 bp
Distance to nearest TSS: 48,734 bp
GENCODE v7 location: Coding region
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'=1.0, r2=0.92

rs10803214
Position: chr1:236,165,216 (Open in UCSC Genome Browser)
Distance to lead SNP: 14,653 bp
Distance to nearest TSS: 58,857 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'=0.958, r2=0.882 / CHB: D'=1.0, r2=0.811 / JPT: D'=1.0, r2=0.842 / YRI: D'=1.0, r2=0.925

rs10754833
Position: chr1:236,184,931 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,062 bp
Distance to nearest TSS: 49,805 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'=0.935, r2=0.823 / YRI: D'=1.0, r2=0.92

rs10737895
Position: chr1:236,185,068 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,199 bp
Distance to nearest TSS: 49,942 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'=0.935, r2=0.823 / YRI: D'=1.0, r2=0.92

rs10803226
Position: chr1:236,184,355 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,486 bp
Distance to nearest TSS: 49,229 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=0.918 / CHB: D'=1.0, r2=1.0 / JPT: D'=0.935, r2=0.823 / YRI: D'=1.0, r2=0.92

rs9662380
Position: chr1:236,178,606 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,263 bp
Distance to nearest TSS: 45,467 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

rs3754237
Position: chr1:236,177,182 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,687 bp
Distance to nearest TSS: 46,891 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=0.942 / 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 01:19:11
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