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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rs588517

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: 8 x 10-06
Gene: RPS7P9 - NRG3
Risk allele: A
Minor allele frequency (controls): 0.15

Lead SNP

rs588517
Position: chr10:83,153,246 (Open in UCSC Genome Browser)
Distance to nearest TSS: 739,757 bp
GENCODE v7 location: Intergenic region
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:

rs265473
Position: chr10:83,147,040 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,206 bp
Distance to nearest TSS: 733,551 bp
GENCODE v7 location: Intergenic region
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=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs1999110
Position: chr10:83,178,570 (Open in UCSC Genome Browser)
Distance to lead SNP: 25,324 bp
Distance to nearest TSS: 765,081 bp
GENCODE v7 location: Intergenic region
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=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs265502
Position: chr10:83,142,270 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,976 bp
Distance to nearest TSS: 728,781 bp
GENCODE v7 location: Intergenic region
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=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs10732784
Position: chr10:83,182,274 (Open in UCSC Genome Browser)
Distance to lead SNP: 29,028 bp
Distance to nearest TSS: 768,785 bp
GENCODE v7 location: Intergenic region
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=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs10786453
Position: chr10:83,167,858 (Open in UCSC Genome Browser)
Distance to lead SNP: 14,612 bp
Distance to nearest TSS: 754,369 bp
GENCODE v7 location: Intergenic region
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

rs265499
Position: chr10:83,144,287 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,959 bp
Distance to nearest TSS: 730,798 bp
GENCODE v7 location: Intergenic region
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

rs265501
Position: chr10:83,143,065 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,181 bp
Distance to nearest TSS: 729,576 bp
GENCODE v7 location: Intergenic region
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

rs265508
Position: chr10:83,139,922 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,324 bp
Distance to nearest TSS: 726,433 bp
GENCODE v7 location: Intergenic region
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

rs10786438
Position: chr10:83,157,102 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,856 bp
Distance to nearest TSS: 743,613 bp
GENCODE v7 location: Intergenic region
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

rs510550
Position: chr10:83,127,985 (Open in UCSC Genome Browser)
Distance to lead SNP: 25,261 bp
Distance to nearest TSS: 714,496 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.827 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs1576305
Position: chr10:83,172,809 (Open in UCSC Genome Browser)
Distance to lead SNP: 19,563 bp
Distance to nearest TSS: 759,320 bp
GENCODE v7 location: Intergenic region
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

rs265458
Position: chr10:83,134,494 (Open in UCSC Genome Browser)
Distance to lead SNP: 18,752 bp
Distance to nearest TSS: 721,005 bp
GENCODE v7 location: Intergenic region
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

rs587253
Position: chr10:83,153,472 (Open in UCSC Genome Browser)
Distance to lead SNP: 226 bp
Distance to nearest TSS: 739,983 bp
GENCODE v7 location: Intergenic region
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

rs1854463
Position: chr10:83,131,664 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,582 bp
Distance to nearest TSS: 718,175 bp
GENCODE v7 location: Intergenic region
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




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 01:19:20
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