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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rs215614

Associations

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 10-07
Odds ratio [95% confidence interval]: .22 [0.14-0.30] CPD increase
Gene: PDE1C - SLC25A5P5
Risk allele: G
Minor allele frequency (controls): 0.36

Lead SNP

rs215614
Position: chr7:32,347,335 (Open in UCSC Genome Browser)
Distance to nearest TSS: 181,581 bp
GENCODE v7 location: Intergenic 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:

rs1668389
Position: chr7:32,386,915 (Open in UCSC Genome Browser)
Distance to lead SNP: 39,580 bp
Distance to nearest TSS: 142,001 bp
GENCODE v7 location: Intergenic region
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=0.953 / CHB: D'=0.884, r2=0.741 / JPT: D'=0.935, r2=0.822

rs215692
Position: chr7:32,394,858 (Open in UCSC Genome Browser)
Distance to lead SNP: 47,523 bp
Distance to nearest TSS: 134,058 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=0.958

rs215605
Position: chr7:32,336,965 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,370 bp
Distance to nearest TSS: 226,959 bp
GENCODE v7 location: Intron
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=0.898 / JPT: D'=1.0, r2=0.847

rs215625
Position: chr7:32,358,313 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,978 bp
Distance to nearest TSS: 170,603 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=0.919 / CHB: D'=1.0, r2=0.775 / JPT: D'=1.0, r2=0.635

rs215639
Position: chr7:32,373,639 (Open in UCSC Genome Browser)
Distance to lead SNP: 26,304 bp
Distance to nearest TSS: 155,277 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=0.906 / CHB: D'=1.0, r2=0.845 / JPT: D'=1.0, r2=0.635

rs215694
Position: chr7:32,397,026 (Open in UCSC Genome Browser)
Distance to lead SNP: 49,691 bp
Distance to nearest TSS: 131,890 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.951, r2=0.905 / CHB: D'=0.878, r2=0.77 / JPT: D'=0.937, r2=0.828

rs412876
Position: chr7:32,395,660 (Open in UCSC Genome Browser)
Distance to lead SNP: 48,325 bp
Distance to nearest TSS: 133,256 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=0.959 / CHB: D'=0.835, r2=0.697 / JPT: D'=0.943, r2=0.842

rs6955346
Position: chr7:32,369,553 (Open in UCSC Genome Browser)
Distance to lead SNP: 22,218 bp
Distance to nearest TSS: 159,363 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=0.916 / CHB: D'=1.0, r2=0.775 / JPT: D'=1.0, r2=0.577

rs215670
Position: chr7:32,379,218 (Open in UCSC Genome Browser)
Distance to lead SNP: 31,883 bp
Distance to nearest TSS: 149,698 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=0.916 / CHB: D'=1.0, r2=0.949 / JPT: D'=1.0, r2=1.0

rs1653889
Position: chr7:32,386,653 (Open in UCSC Genome Browser)
Distance to lead SNP: 39,318 bp
Distance to nearest TSS: 142,263 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.953, r2=0.907 / CHB: D'=0.884, r2=0.741 / JPT: D'=0.879, r2=0.773

rs1668393
Position: chr7:32,393,611 (Open in UCSC Genome Browser)
Distance to lead SNP: 46,276 bp
Distance to nearest TSS: 135,305 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.952, r2=0.907 / CHB: D'=0.884, r2=0.741 / JPT: D'=0.88, r2=0.663

rs215611
Position: chr7:32,341,438 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,897 bp
Distance to nearest TSS: 187,478 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.958 / CHB: D'=1.0, r2=0.849 / JPT: D'=1.0, r2=0.947

rs215669
Position: chr7:32,378,979 (Open in UCSC Genome Browser)
Distance to lead SNP: 31,644 bp
Distance to nearest TSS: 149,937 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.959 / CHB: D'=0.942, r2=0.84 / JPT: D'=1.0, r2=0.947

rs215622
Position: chr7:32,357,659 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,324 bp
Distance to nearest TSS: 171,257 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.919 / CHB: D'=1.0, r2=0.775 / JPT: D'=1.0, r2=0.635

rs215629
Position: chr7:32,360,464 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,129 bp
Distance to nearest TSS: 168,452 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.917 / CHB: D'=1.0, r2=0.738 / JPT: D'=1.0, r2=0.577

rs215632
Position: chr7:32,368,524 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,189 bp
Distance to nearest TSS: 160,392 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

rs215634
Position: chr7:32,369,148 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,813 bp
Distance to nearest TSS: 159,768 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.959 / CHB: D'=1.0, r2=0.849 / JPT: D'=1.0, r2=0.947

rs186229
Position: chr7:32,381,557 (Open in UCSC Genome Browser)
Distance to lead SNP: 34,222 bp
Distance to nearest TSS: 147,359 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.959 / CHB: D'=0.888, r2=0.789 / JPT: D'=0.943, r2=0.842




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 01:19:18
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