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

rs11661542

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]: 1.22 [1.15-1.28]
Gene: RPS4XP18 - RBBP8
Risk allele: C
Minor allele frequency (controls): 0.49

Lead SNP

rs11661542
Position: chr18:20,223,695 (Open in UCSC Genome Browser)
Distance to nearest TSS: 13,335,275 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5a - ChIP-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:

rs13381302
Position: chr18:20,211,128 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,567 bp
Distance to nearest TSS: 13,347,842 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5a - ChIP-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=1.0

rs12326842
Position: chr18:20,205,437 (Open in UCSC Genome Browser)
Distance to lead SNP: 18,258 bp
Distance to nearest TSS: 13,353,533 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5a - ChIP-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=1.0

rs8096784
Position: chr18:20,186,934 (Open in UCSC Genome Browser)
Distance to lead SNP: 36,761 bp
Distance to nearest TSS: 13,372,036 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.951 / YRI: D'=1.0, r2=1.0

rs12953657
Position: chr18:20,192,907 (Open in UCSC Genome Browser)
Distance to lead SNP: 30,788 bp
Distance to nearest TSS: 13,366,063 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.953 / YRI: D'=1.0, r2=1.0

rs10853450
Position: chr18:20,235,681 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,986 bp
Distance to nearest TSS: 13,323,289 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

rs12959243
Position: chr18:20,206,802 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,893 bp
Distance to nearest TSS: 13,352,168 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

rs11661377
Position: chr18:20,195,446 (Open in UCSC Genome Browser)
Distance to lead SNP: 28,249 bp
Distance to nearest TSS: 13,363,524 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=0.95 / YRI: D'=1.0, r2=1.0

rs10853448
Position: chr18:20,230,111 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,416 bp
Distance to nearest TSS: 13,328,859 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.889 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs4530259
Position: chr18:20,196,334 (Open in UCSC Genome Browser)
Distance to lead SNP: 27,361 bp
Distance to nearest TSS: 13,362,636 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

rs11661464
Position: chr18:20,218,126 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,569 bp
Distance to nearest TSS: 13,340,844 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

rs1879713
Position: chr18:20,205,248 (Open in UCSC Genome Browser)
Distance to lead SNP: 18,447 bp
Distance to nearest TSS: 13,353,722 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

rs1879714
Position: chr18:20,208,786 (Open in UCSC Genome Browser)
Distance to lead SNP: 14,909 bp
Distance to nearest TSS: 13,350,184 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

rs9653003
Position: chr18:20,196,110 (Open in UCSC Genome Browser)
Distance to lead SNP: 27,585 bp
Distance to nearest TSS: 13,362,860 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

rs9789208
Position: chr18:20,210,259 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,436 bp
Distance to nearest TSS: 13,348,711 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

rs11082051
Position: chr18:20,234,336 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,641 bp
Distance to nearest TSS: 13,324,634 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

rs4267433
Position: chr18:20,202,885 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,810 bp
Distance to nearest TSS: 13,356,085 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 01:19:24
SCGPM logo A project of the Center for Genomics and Personalized Medicine at Stanford University. Stanford logo