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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rs9298506

Associations

Study: Genome-wide association study of intracranial aneurysm identifies three new risk loci. [PMID:20364137]
First author: Yasuno K
Journal: Nat Genet
Date: 04/04/2010
Phenotype: Intracranial aneurysm
Study population: 2,780 European cases, 12,515 European controls
Replication population: 3,111 Japanese cases, 1,666 Japanese controls
Association P-value: 1 x 10-12
Odds ratio [95% confidence interval]: 1.28 [1.20-1.38]
Gene: SEC11B - RP1
Risk allele: A
Minor allele frequency (controls): 0.81

Study: Susceptibility loci for intracranial aneurysm in European and Japanese populations. [PMID:18997786]
First author: Bilguvar K
Journal: Nat Genet
Date: 11/09/2008
Phenotype: Intracranial aneurysm
Study population: 1,580 European cases,6,276 European controls
Replication population: 495 Japanese cases,676 Japanese controls
Association P-value: 2 x 10-09
Odds ratio [95% confidence interval]: 1.35 [1.22-1.49]
Gene: SEC11B - RP1
Risk allele: A
Minor allele frequency (controls): 0.81

Lead SNP

rs9298506
Position: chr8:55,437,524 (Open in UCSC Genome Browser)
Distance to nearest TSS: 36,944 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - 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:

rs10102164
Position: chr8:55,421,614 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,910 bp
Distance to nearest TSS: 49,058 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=0.94

rs10104003
Position: chr8:55,422,440 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,084 bp
Distance to nearest TSS: 49,884 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=0.94

rs10104997
Position: chr8:55,440,068 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,544 bp
Distance to nearest TSS: 34,400 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=0.885

rs10103996
Position: chr8:55,422,424 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,100 bp
Distance to nearest TSS: 49,868 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.932 / CHB: D'=1.0, r2=0.933 / JPT: D'=1.0, r2=0.93 / 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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