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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rs7553864

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]: .08 [NR] more years
Gene: HS2ST1 - LMO4
Minor allele frequency (controls): 0.39

Lead SNP

rs7553864
Position: chr1:87,613,358 (Open in UCSC Genome Browser)
Distance to nearest TSS: 11,005 bp
GENCODE v7 location: Intron
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:

rs6576866
Position: chr1:87,601,471 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,887 bp
Distance to nearest TSS: 1,725 bp
GENCODE v7 location: Exon, non-coding
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.957, r2=0.812 / CHB: D'=1.0, r2=0.897 / JPT: D'=0.911, r2=0.764 / YRI: D'=0.903, r2=0.525

rs2807946
Position: chr1:87,597,457 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,901 bp
Distance to nearest TSS: 27,077 bp
GENCODE v7 location: Intron
RegulomeDB Score: 4 - ChIP-seq peak + DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.961 / CHB: D'=1.0, r2=1.0 / JPT: D'=0.906, r2=0.647

rs7539833
Position: chr1:87,613,228 (Open in UCSC Genome Browser)
Distance to lead SNP: 130 bp
Distance to nearest TSS: 10,875 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=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.795, r2=0.584

rs10873820
Position: chr1:87,605,973 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,385 bp
Distance to nearest TSS: 11,156 bp
GENCODE v7 location: Intron
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.957, r2=0.812 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.85

rs7515367
Position: chr1:87,615,798 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,440 bp
Distance to nearest TSS: 13,445 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=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.663

rs4551571
Position: chr1:87,614,244 (Open in UCSC Genome Browser)
Distance to lead SNP: 886 bp
Distance to nearest TSS: 11,891 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.812 / CHB: D'=1.0, r2=0.904 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.507

rs719015
Position: chr1:87,611,710 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,648 bp
Distance to nearest TSS: 9,357 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.924 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.832 / YRI: D'=1.0, r2=0.594

rs7512650
Position: chr1:87,609,076 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,282 bp
Distance to nearest TSS: 8,053 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.957, r2=0.812 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.85

rs4415539
Position: chr1:87,604,245 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,113 bp
Distance to nearest TSS: 12,884 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=0.897 / JPT: D'=0.911, r2=0.764

rs1886633
Position: chr1:87,610,356 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,002 bp
Distance to nearest TSS: 8,003 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.956, r2=0.808 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=0.85

rs975038
Position: chr1:87,613,583 (Open in UCSC Genome Browser)
Distance to lead SNP: 225 bp
Distance to nearest TSS: 11,230 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=1.0 / JPT: D'=1.0, r2=0.833 / YRI: D'=0.779, r2=0.582

rs11161935
Position: chr1:87,614,191 (Open in UCSC Genome Browser)
Distance to lead SNP: 833 bp
Distance to nearest TSS: 11,838 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0 / YRI: D'=0.721, r2=0.52




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 01:19:10
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