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:

rs8040868
Position: chr15:78,911,181 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,842 bp
Distance to nearest TSS: 16,605 bp
GENCODE v7 location: Coding region
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.888

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

rs17405217
Position: chr15:78,731,149 (Open in UCSC Genome Browser)
Distance to lead SNP: 163,190 bp
Distance to nearest TSS: 90,829 bp
GENCODE v7 location: Intron
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.809 / CHB: D'=1.0, r2=0.741 / JPT: D'=1.0, r2=1.0

rs17483548
Position: chr15:78,730,313 (Open in UCSC Genome Browser)
Distance to lead SNP: 164,026 bp
Distance to nearest TSS: 89,993 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.809 / CHB: D'=1.0, r2=0.741 / JPT: D'=1.0, r2=1.0

rs7181486
Position: chr15:78,741,618 (Open in UCSC Genome Browser)
Distance to lead SNP: 152,721 bp
Distance to nearest TSS: 101,298 bp
GENCODE v7 location: Intron
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.809

rs2009746
Position: chr15:78,754,102 (Open in UCSC Genome Browser)
Distance to lead SNP: 140,237 bp
Distance to nearest TSS: 113,782 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.914, r2=0.802

rs2568494
Position: chr15:78,740,964 (Open in UCSC Genome Browser)
Distance to lead SNP: 153,375 bp
Distance to nearest TSS: 100,644 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.809

rs2036527
Position: chr15:78,851,615 (Open in UCSC Genome Browser)
Distance to lead SNP: 42,724 bp
Distance to nearest TSS: 31,217 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=0.961 / CHB: D'=1.0, r2=0.741 / JPT: D'=1.0, r2=1.0

rs2656052
Position: chr15:78,740,932 (Open in UCSC Genome Browser)
Distance to lead SNP: 153,407 bp
Distance to nearest TSS: 100,612 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.809

rs17487223
Position: chr15:78,923,987 (Open in UCSC Genome Browser)
Distance to lead SNP: 29,648 bp
Distance to nearest TSS: 10,850 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.81 / CHB: D'=1.0, r2=1.0

rs17483929
Position: chr15:78,742,376 (Open in UCSC Genome Browser)
Distance to lead SNP: 151,963 bp
Distance to nearest TSS: 102,056 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.809

rs10519203
Position: chr15:78,814,046 (Open in UCSC Genome Browser)
Distance to lead SNP: 80,293 bp
Distance to nearest TSS: 11,967 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961

rs9788721
Position: chr15:78,802,869 (Open in UCSC Genome Browser)
Distance to lead SNP: 91,470 bp
Distance to nearest TSS: 12,383 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961

rs17483721
Position: chr15:78,733,731 (Open in UCSC Genome Browser)
Distance to lead SNP: 160,608 bp
Distance to nearest TSS: 93,411 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.809

rs2656065
Position: chr15:78,750,549 (Open in UCSC Genome Browser)
Distance to lead SNP: 143,790 bp
Distance to nearest TSS: 110,229 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.914, r2=0.8

rs12914385
Position: chr15:78,898,723 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,384 bp
Distance to nearest TSS: 14,414 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.924

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

rs17484524
Position: chr15:78,772,676 (Open in UCSC Genome Browser)
Distance to lead SNP: 121,663 bp
Distance to nearest TSS: 132,356 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.914, r2=0.802 / CHB: D'=1.0, r2=0.741 / JPT: D'=1.0, r2=1.0

rs17484235
Position: chr15:78,761,414 (Open in UCSC Genome Browser)
Distance to lead SNP: 132,925 bp
Distance to nearest TSS: 121,094 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.809 / CHB: D'=1.0, r2=0.741 / JPT: D'=1.0, r2=1.0

rs1504550
Position: chr15:78,766,250 (Open in UCSC Genome Browser)
Distance to lead SNP: 128,089 bp
Distance to nearest TSS: 125,930 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.918, r2=0.809 / CHB: D'=1.0, r2=0.741 / JPT: D'=1.0, r2=1.0

rs8031948
Position: chr15:78,816,057 (Open in UCSC Genome Browser)
Distance to lead SNP: 78,282 bp
Distance to nearest TSS: 9,956 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.96 / CHB: D'=1.0, r2=0.741 / JPT: 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

rs931794
Position: chr15:78,826,180 (Open in UCSC Genome Browser)
Distance to lead SNP: 68,159 bp
Distance to nearest TSS: 3,464 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961

rs8034191
Position: chr15:78,806,023 (Open in UCSC Genome Browser)
Distance to lead SNP: 88,316 bp
Distance to nearest TSS: 15,537 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=0.741 / JPT: 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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