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: 3 x 10-06
Odds ratio [95% confidence interval]: .12 [NR] more pack years
Gene: C3orf58 - GM2AP1
Minor allele frequency (controls): 0.42
rs800082
Position: chr3:144,340,205
(Open in UCSC Genome Browser)
Distance to nearest TSS: 1,274,956 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
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:
rs1405597
Position: chr3:144,314,276
(Open in UCSC Genome Browser)
Distance to lead SNP: 25,929 bp
Distance to nearest TSS: 1,300,885 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=1.0 / CHB: D'=1.0, r2=0.761 / JPT: D'=1.0, r2=1.0
rs11718059
Position: chr3:144,305,997
(Open in UCSC Genome Browser)
Distance to lead SNP: 34,208 bp
Distance to nearest TSS: 1,309,164 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=1.0 / CHB: D'=1.0, r2=0.932 / JPT: D'=1.0, r2=1.0
rs12637885
Position: chr3:144,291,254
(Open in UCSC Genome Browser)
Distance to lead SNP: 48,951 bp
Distance to nearest TSS: 1,323,907 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
rs800084
Position: chr3:144,340,494
(Open in UCSC Genome Browser)
Distance to lead SNP: 289 bp
Distance to nearest TSS: 1,274,667 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
rs9882503
Position: chr3:144,321,296
(Open in UCSC Genome Browser)
Distance to lead SNP: 18,909 bp
Distance to nearest TSS: 1,293,865 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 / YRI: D'=1.0, r2=0.521
rs9289678
Position: chr3:144,307,096
(Open in UCSC Genome Browser)
Distance to lead SNP: 33,109 bp
Distance to nearest TSS: 1,308,065 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
rs4681363
Position: chr3:144,287,355
(Open in UCSC Genome Browser)
Distance to lead SNP: 52,850 bp
Distance to nearest TSS: 1,327,806 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
rs1405599
Position: chr3:144,328,759
(Open in UCSC Genome Browser)
Distance to lead SNP: 11,446 bp
Distance to nearest TSS: 1,286,402 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.521
rs4681378
Position: chr3:144,308,005
(Open in UCSC Genome Browser)
Distance to lead SNP: 32,200 bp
Distance to nearest TSS: 1,307,156 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
rs6440259
Position: chr3:144,286,614
(Open in UCSC Genome Browser)
Distance to lead SNP: 53,591 bp
Distance to nearest TSS: 1,328,547 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=0.761 / JPT: D'=1.0, r2=1.0
rs7613909
Position: chr3:144,308,606
(Open in UCSC Genome Browser)
Distance to lead SNP: 31,599 bp
Distance to nearest TSS: 1,306,555 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.521
rs9817588
Position: chr3:144,288,302
(Open in UCSC Genome Browser)
Distance to lead SNP: 51,903 bp
Distance to nearest TSS: 1,326,859 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: 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.