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

Return Home

rs9315204

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: 3 x 10-09
Odds ratio [95% confidence interval]: 1.20 [1.13-1.28]
Gene: STARD13
Risk allele: T
Minor allele frequency (controls): 0.21

Lead SNP

rs9315204
Position: chr13:33,693,837 (Open in UCSC Genome Browser)
Distance to nearest TSS: 55,396 bp
GENCODE v7 location: Intron
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:

rs3742321
Position: chr13:33,704,065 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,228 bp
Distance to nearest TSS: 12,415 bp
GENCODE v7 location: Coding 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=0.88

rs9536548
Position: chr13:33,723,786 (Open in UCSC Genome Browser)
Distance to lead SNP: 29,949 bp
Distance to nearest TSS: 14,761 bp
GENCODE v7 location: Intron
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=0.88




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 01:19:22
SCGPM logo A project of the Center for Genomics and Personalized Medicine at Stanford University. Stanford logo