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

Return Home

rs933688

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]: 1.48 [NR]
Gene: ARRDC3 - PCBP2P3
Minor allele frequency (controls): 0.17

Lead SNP

rs933688
Position: chr5:90,762,748 (Open in UCSC Genome Browser)
Distance to nearest TSS: 865,654 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:

rs12188467
Position: chr5:90,765,632 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,884 bp
Distance to nearest TSS: 862,770 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.942

rs7715402
Position: chr5:90,679,504 (Open in UCSC Genome Browser)
Distance to lead SNP: 83,244 bp
Distance to nearest TSS: 948,898 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs1541674
Position: chr5:90,660,447 (Open in UCSC Genome Browser)
Distance to lead SNP: 102,301 bp
Distance to nearest TSS: 15,522 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=1.0 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs12110303
Position: chr5:90,662,839 (Open in UCSC Genome Browser)
Distance to lead SNP: 99,909 bp
Distance to nearest TSS: 13,130 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=1.0

rs332531
Position: chr5:90,790,451 (Open in UCSC Genome Browser)
Distance to lead SNP: 27,703 bp
Distance to nearest TSS: 837,951 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=1.0 / CHB: D'=1.0, r2=0.95 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.867, r2=0.569

rs7718871
Position: chr5:90,671,624 (Open in UCSC Genome Browser)
Distance to lead SNP: 91,124 bp
Distance to nearest TSS: 19,780 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=1.0

rs1895448
Position: chr5:90,743,854 (Open in UCSC Genome Browser)
Distance to lead SNP: 18,894 bp
Distance to nearest TSS: 884,548 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=0.954 / JPT: D'=1.0, r2=1.0

rs7720235
Position: chr5:90,659,329 (Open in UCSC Genome Browser)
Distance to lead SNP: 103,419 bp
Distance to nearest TSS: 16,640 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=1.0

rs6862125
Position: chr5:90,724,598 (Open in UCSC Genome Browser)
Distance to lead SNP: 38,150 bp
Distance to nearest TSS: 903,804 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=1.0

rs12655973
Position: chr5:90,736,537 (Open in UCSC Genome Browser)
Distance to lead SNP: 26,211 bp
Distance to nearest TSS: 891,865 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=1.0

rs6865495
Position: chr5:90,746,424 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,324 bp
Distance to nearest TSS: 881,978 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=1.0

rs186717
Position: chr5:90,780,467 (Open in UCSC Genome Browser)
Distance to lead SNP: 17,719 bp
Distance to nearest TSS: 847,935 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=1.0 / YRI: D'=1.0, r2=1.0

rs332544
Position: chr5:90,778,848 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,100 bp
Distance to nearest TSS: 849,554 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

rs12110065
Position: chr5:90,718,474 (Open in UCSC Genome Browser)
Distance to lead SNP: 44,274 bp
Distance to nearest TSS: 909,928 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

rs6867091
Position: chr5:90,734,333 (Open in UCSC Genome Browser)
Distance to lead SNP: 28,415 bp
Distance to nearest TSS: 894,069 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'=0.939, r2=0.881

rs2839728
Position: chr5:90,727,412 (Open in UCSC Genome Browser)
Distance to lead SNP: 35,336 bp
Distance to nearest TSS: 900,990 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'=0.933, r2=0.625

rs2059207
Position: chr5:90,731,931 (Open in UCSC Genome Browser)
Distance to lead SNP: 30,817 bp
Distance to nearest TSS: 896,471 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'=0.939, r2=0.881

rs6452953
Position: chr5:90,723,034 (Open in UCSC Genome Browser)
Distance to lead SNP: 39,714 bp
Distance to nearest TSS: 905,368 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'=0.934, r2=0.659

rs10045280
Position: chr5:90,717,675 (Open in UCSC Genome Browser)
Distance to lead SNP: 45,073 bp
Distance to nearest TSS: 910,727 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'=0.928, r2=0.636

rs6866923
Position: chr5:90,669,352 (Open in UCSC Genome Browser)
Distance to lead SNP: 93,396 bp
Distance to nearest TSS: 17,508 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=0.95

rs1363839
Position: chr5:90,671,274 (Open in UCSC Genome Browser)
Distance to lead SNP: 91,474 bp
Distance to nearest TSS: 19,430 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




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 01:19:15
SCGPM logo A project of the Center for Genomics and Personalized Medicine at Stanford University. Stanford logo