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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rs800082

Associations

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

Lead SNP

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 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:

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

Contact: marc.schaub AT cs.stanford.edu
Last modified: 2011-12-15 01:19:13
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