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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rs17151904

Associations

Study: A genome-wide association study of carotid atherosclerosis in HIV-infected men. [PMID:20009918]
First author: Shrestha S
Journal: AIDS
Date: 01/01/2010
Phenotype: Carotid atherosclerosis in HIV infection
Study population: 177 Caucasian HIV-infected men
Association P-value: 1 x 10-06
Gene: NPVF - UBA52P1
Risk allele: A
Minor allele frequency (controls): 0.20

Lead SNP

rs17151904
Position: chr7:25,608,409 (Open in UCSC Genome Browser)
Distance to nearest TSS: 17,726 bp
GENCODE v7 location: Intergenic region
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:

rs11973620
Position: chr7:25,608,070 (Open in UCSC Genome Browser)
Distance to lead SNP: 339 bp
Distance to nearest TSS: 17,387 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.94 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / 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 01:19:18
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