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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rs1402279

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: 5 x 10-06
Odds ratio [95% confidence interval]: 1.51 [NR]
Gene: E2F7 - NAV3
Minor allele frequency (controls): 0.95

Lead SNP

rs1402279
Position: chr12:77,729,385 (Open in UCSC Genome Browser)
Distance to nearest TSS: 236,662 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:

rs1798746
Position: chr12:77,687,760 (Open in UCSC Genome Browser)
Distance to lead SNP: 41,625 bp
Distance to nearest TSS: 278,287 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'=1.0, r2=0.825 / YRI: D'=0.892, r2=0.52

rs939449
Position: chr12:77,700,750 (Open in UCSC Genome Browser)
Distance to lead SNP: 28,635 bp
Distance to nearest TSS: 265,297 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5a - ChIP-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.825 / CHB: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.857

rs1798747
Position: chr12:77,687,514 (Open in UCSC Genome Browser)
Distance to lead SNP: 41,871 bp
Distance to nearest TSS: 278,533 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=0.825

rs879360
Position: chr12:77,701,277 (Open in UCSC Genome Browser)
Distance to lead SNP: 28,108 bp
Distance to nearest TSS: 264,770 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=0.825 / CHB: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.848

rs1568430
Position: chr12:77,726,311 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,074 bp
Distance to nearest TSS: 239,736 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=0.563

rs1081560
Position: chr12:77,682,346 (Open in UCSC Genome Browser)
Distance to lead SNP: 47,039 bp
Distance to nearest TSS: 283,701 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=0.825

rs6538132
Position: chr12:77,722,909 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,476 bp
Distance to nearest TSS: 243,138 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=0.633

rs1568432
Position: chr12:77,696,666 (Open in UCSC Genome Browser)
Distance to lead SNP: 32,719 bp
Distance to nearest TSS: 269,381 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.825 / CHB: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.857

rs1520700
Position: chr12:77,687,384 (Open in UCSC Genome Browser)
Distance to lead SNP: 42,001 bp
Distance to nearest TSS: 278,663 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.825 / YRI: D'=1.0, r2=0.587

rs1520701
Position: chr12:77,698,505 (Open in UCSC Genome Browser)
Distance to lead SNP: 30,880 bp
Distance to nearest TSS: 267,542 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=0.524

rs4761306
Position: chr12:77,727,393 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,992 bp
Distance to nearest TSS: 238,654 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 01:19:21
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