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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rs1051730

Associations

Study: Meta-analysis and imputation refines the association of 15q25 with smoking quantity. [PMID:20418889]
First author: Liu JZ
Journal: Nat Genet
Date: 04/25/2010
Phenotype: Smoking behavior
Study population: 41,150 European descent individuals
Replication population: 120,516 European descent individuals
Association P-value: 2 x 10-66
Odds ratio [95% confidence interval]: .08 [0.07-0.09] unit decrease
Gene: CHRNA3
Risk allele: G
Minor allele frequency (controls): 0.66

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: 3 x 10-73
Odds ratio [95% confidence interval]: 1.02 [0.91-1.13] CPD decrease
Gene: CHRNA3
Risk allele: G
Minor allele frequency (controls): 0.65

Study: Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior. [PMID:20418888]
First author: Thorgeirsson TE
Journal: Nat Genet
Date: 04/25/2010
Phenotype: Smoking behavior
Study population: 31,266 European ancestry individuals
Replication population: 54,731 European descent individuals
Association P-value: 2 x 10-69
Odds ratio [95% confidence interval]: .80 [0.70-0.90] CPD increase
Gene: CHRNA3
Risk allele: A
Minor allele frequency (controls): 0.34

Study: A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. [PMID:19836008]
First author: Landi MT
Journal: Am J Hum Genet
Date: 10/15/2009
Phenotype: Lung adenocarcinoma
Study population: 5,739 European descent cases, 5,848 European descent controls
Replication population: 7,561 European descent cases, 13,818 European descent controls
Association P-value: 2 x 10-51
Odds ratio [95% confidence interval]: 1.31 [1.27-1.36]
Gene: CHRNA3
Risk allele: T
Minor allele frequency (controls): 0.35

Study: Lung cancer susceptibility locus at 5p15.33. [PMID:18978790]
First author: McKay JD
Journal: Nat Genet
Date: 11/02/2008
Phenotype: Lung cancer
Study population: 2,971 cases,3,746 controls
Replication population: 2,899 cases,5,573 controls
Association P-value: 1 x 10-15
Odds ratio [95% confidence interval]: 1.35 [1.25-1.45]
Gene: CHRNA3
Risk allele: A

Study: A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. [PMID:18385739]
First author: Thorgeirsson TE
Journal: Nature
Date: 04/03/2008
Phenotype: Nicotine dependence
Study population: 10,995 smokers
Replication population: 4,848 smokers
Association P-value: 6 x 10-20
Odds ratio [95% confidence interval]: .10 [0.08-0.12] increase in cigarettes per day
Gene: CHRNA3
Risk allele: T
Minor allele frequency (controls): 0.35

Lead SNP

rs1051730
Position: chr15:78,894,339 (Open in UCSC Genome Browser)
Distance to nearest TSS: 8,743 bp
GENCODE v7 location: Coding region
RegulomeDB Score: 6 - Motif (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:

rs16969968
Position: chr15:78,882,925 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,414 bp
Distance to nearest TSS: 2,671 bp
GENCODE v7 location: Coding 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=1.0

rs17486278
Position: chr15:78,867,482 (Open in UCSC Genome Browser)
Distance to lead SNP: 26,857 bp
Distance to nearest TSS: 26,195 bp
GENCODE v7 location: Intron
RegulomeDB Score: 2b - ChIP-seq peak + any motif + matched DNase Footprint + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0

rs951266
Position: chr15:78,878,541 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,798 bp
Distance to nearest TSS: 37,254 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=1.0

rs1317286
Position: chr15:78,896,129 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,790 bp
Distance to nearest TSS: 17,008 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

rs7180002
Position: chr15:78,873,993 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,346 bp
Distance to nearest TSS: 32,706 bp
GENCODE v7 location: Intron
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 01:19:23
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