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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rs912969

Associations

Study: Genome-wide and candidate gene association study of cigarette smoking behaviors. [PMID:19247474]
First author: Caporaso N
Journal: PLoS One
Date: 02/27/2009
Phenotype: Smoking behavior
Study population: 4,611 individuals (2,617 smokers)
Association P-value: 8 x 10-06
Odds ratio [95% confidence interval]: .14 [NR] fewer years
Gene: SLC10A2 - RPL7P45
Minor allele frequency (controls): 0.07

Lead SNP

rs912969
Position: chr13:103,867,104 (Open in UCSC Genome Browser)
Distance to nearest TSS: 212,932 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:

rs1730663
Position: chr13:103,868,593 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,489 bp
Distance to nearest TSS: 211,443 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=0.912

rs1750427
Position: chr13:103,867,230 (Open in UCSC Genome Browser)
Distance to lead SNP: 126 bp
Distance to nearest TSS: 212,806 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=0.912

rs2806324
Position: chr13:103,866,056 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,048 bp
Distance to nearest TSS: 213,980 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.918

rs927798
Position: chr13:103,868,004 (Open in UCSC Genome Browser)
Distance to lead SNP: 900 bp
Distance to nearest TSS: 212,032 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=0.928 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs1730662
Position: chr13:103,867,903 (Open in UCSC Genome Browser)
Distance to lead SNP: 799 bp
Distance to nearest TSS: 212,133 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.912




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
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