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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rs10411195

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]: .21 [NR] fewer cigarettes per day
Gene: ZNF93
Minor allele frequency (controls): 0.03

Lead SNP

rs10411195
Position: chr19:20,036,176 (Open in UCSC Genome Browser)
Distance to nearest TSS: 27,596 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:

rs10407807
Position: chr19:20,046,102 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,926 bp
Distance to nearest TSS: 759 bp
GENCODE v7 location: Exon, non-coding
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 / YRI: D'=1.0, r2=0.745

rs10422520
Position: chr19:19,887,369 (Open in UCSC Genome Browser)
Distance to lead SNP: 148,807 bp
Distance to nearest TSS: 45,044 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 2a - ChIP-seq peak + matched TF motif + matched Dnase Footprint + 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=0.888

rs2215914
Position: chr19:20,023,643 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,533 bp
Distance to nearest TSS: 21,985 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs10403362
Position: chr19:19,879,757 (Open in UCSC Genome Browser)
Distance to lead SNP: 156,419 bp
Distance to nearest TSS: 23,930 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=1.0 / JPT: D'=1.0, r2=0.796

rs7254125
Position: chr19:20,036,615 (Open in UCSC Genome Browser)
Distance to lead SNP: 439 bp
Distance to nearest TSS: 28,035 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

rs10419205
Position: chr19:19,987,491 (Open in UCSC Genome Browser)
Distance to lead SNP: 48,685 bp
Distance to nearest TSS: 55,078 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=0.65 / JPT: D'=1.0, r2=1.0

rs10416399
Position: chr19:20,046,926 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,750 bp
Distance to nearest TSS: 70,394 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=0.65 / JPT: D'=1.0, r2=0.596

rs10419102
Position: chr19:20,017,738 (Open in UCSC Genome Browser)
Distance to lead SNP: 18,438 bp
Distance to nearest TSS: 27,890 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=1.0 / YRI: D'=1.0, r2=0.744

rs1303719
Position: chr19:20,017,390 (Open in UCSC Genome Browser)
Distance to lead SNP: 18,786 bp
Distance to nearest TSS: 28,238 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=1.0 / YRI: D'=1.0, r2=1.0

rs10414768
Position: chr19:20,055,370 (Open in UCSC Genome Browser)
Distance to lead SNP: 19,194 bp
Distance to nearest TSS: 61,950 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 / YRI: D'=1.0, r2=0.924

rs919784
Position: chr19:19,953,210 (Open in UCSC Genome Browser)
Distance to lead SNP: 82,966 bp
Distance to nearest TSS: 50,347 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=0.888

rs2192619
Position: chr19:20,009,528 (Open in UCSC Genome Browser)
Distance to lead SNP: 26,648 bp
Distance to nearest TSS: 36,100 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 / YRI: D'=1.0, r2=1.0

rs2192622
Position: chr19:20,009,739 (Open in UCSC Genome Browser)
Distance to lead SNP: 26,437 bp
Distance to nearest TSS: 35,889 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 / YRI: D'=1.0, r2=0.924

rs10405744
Position: chr19:20,059,493 (Open in UCSC Genome Browser)
Distance to lead SNP: 23,317 bp
Distance to nearest TSS: 57,827 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=0.758 / YRI: D'=0.918, r2=0.843

rs11881577
Position: chr19:20,039,068 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,892 bp
Distance to nearest TSS: 30,488 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=1.0 / YRI: D'=1.0, r2=0.745




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 01:19:24
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