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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rs1329650

Associations

Study: Genome-wide meta-analyses identify multiple loci associated with smoking behavior. [PMID:20418890]
First author: The Tobacco and Genetics Consortium
Journal: Nat Genet
Date: 04/25/2010
Phenotype: Smoking behavior
Study population: Up to 74,035 European ancestry individuals
Replication population: Up to 68,988 participants
Association P-value: 6 x 10-10
Odds ratio [95% confidence interval]: .37 [0.25-0.49] CPD decrease
Gene: RPS27P1 - PPP1R3C
Risk allele: T
Minor allele frequency (controls): 0.28

Lead SNP

rs1329650
Position: chr10:93,348,120 (Open in UCSC Genome Browser)
Distance to nearest TSS: 75,978 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 4 - ChIP-seq peak + 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 

No SNPs found for this LD threshold.




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 01:19:20
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