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
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 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
RegulomeDB (TM) Copyright ©2011 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied. The RegulomeDB project at Stanford University is supported by a Genome Research Resource Grant from the US National Human Genome Research Institute, part of the US National Institutes of Health.