rs933688

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: 6 x 10^-06
Odds ratio [95% confidence interval]: 1.48 [NR]
Gene: ARRDC3 - PCBP2P3
Minor allele frequency (controls): 0.17

Lead SNP

rs933688
Position: chr5:90,762,748 (Open in UCSC Genome Browser)
Distance to nearest TSS: 865,654 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:

rs186717
Position: chr5:90,780,467 (Open in UCSC Genome Browser)
Distance to lead SNP: 17,719 bp
Distance to nearest TSS: 847,935 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

rs332544
Position: chr5:90,778,848 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,100 bp
Distance to nearest TSS: 849,554 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