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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rs1889899

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: 6 x 10-06
Odds ratio [95% confidence interval]: 1.26 [NR]
Gene: TUSC1 - C9orf82
Minor allele frequency (controls): 0.37

Lead SNP

rs1889899
Position: chr9:26,789,940 (Open in UCSC Genome Browser)
Distance to nearest TSS: 6,363 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (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:

rs12684342
Position: chr9:26,782,630 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,310 bp
Distance to nearest TSS: 998,069 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5a - ChIP-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.96 / CHB: D'=1.0, r2=0.824 / JPT: D'=1.0, r2=0.805 / YRI: D'=0.884, r2=0.74

rs892568
Position: chr9:26,773,401 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,539 bp
Distance to nearest TSS: 988,840 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=0.694 / JPT: D'=1.0, r2=0.742

rs10812465
Position: chr9:26,792,671 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,731 bp
Distance to nearest TSS: 5,798 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=0.924 / YRI: D'=0.884, r2=0.634

rs10116852
Position: chr9:26,796,160 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,220 bp
Distance to nearest TSS: 9,287 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=0.924 / YRI: D'=0.876, r2=0.618

rs10114193
Position: chr9:26,796,657 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,717 bp
Distance to nearest TSS: 9,204 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=0.92 / YRI: D'=0.884, r2=0.634

rs10967533
Position: chr9:26,781,145 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,795 bp
Distance to nearest TSS: 996,584 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=0.824 / JPT: D'=1.0, r2=0.863 / YRI: D'=0.884, r2=0.739

rs10511775
Position: chr9:26,788,498 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,442 bp
Distance to nearest TSS: 7,805 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=0.824 / JPT: D'=1.0, r2=0.863 / YRI: D'=1.0, r2=0.899

rs10511778
Position: chr9:26,773,306 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,634 bp
Distance to nearest TSS: 988,745 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=0.822 / JPT: D'=1.0, r2=0.855

rs1434486
Position: chr9:26,782,507 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,433 bp
Distance to nearest TSS: 997,946 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=0.824 / JPT: D'=1.0, r2=0.863 / YRI: D'=0.884, r2=0.74




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 01:19:19
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