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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rs6474412

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: 1 x 10-08
Odds ratio [95% confidence interval]: .29 [0.19-0.39] CPD increase
Gene: C8orf40 - CHRNB3
Risk allele: T
Minor allele frequency (controls): 0.78

Lead SNP

rs6474412
Position: chr8:42,550,498 (Open in UCSC Genome Browser)
Distance to nearest TSS: 142,746 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:

rs4950
Position: chr8:42,552,633 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,135 bp
Distance to nearest TSS: 144,881 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=0.933 / JPT: D'=1.0, r2=1.0

rs13280604
Position: chr8:42,559,586 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,088 bp
Distance to nearest TSS: 151,834 bp
GENCODE v7 location: Exon, non-coding
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=0.933 / JPT: D'=1.0, r2=1.0

rs1530848
Position: chr8:42,552,908 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,410 bp
Distance to nearest TSS: 145,156 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=1.0 / CHB: D'=1.0, r2=0.867 / JPT: D'=1.0, r2=1.0

rs6474413
Position: chr8:42,551,064 (Open in UCSC Genome Browser)
Distance to lead SNP: 566 bp
Distance to nearest TSS: 143,312 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=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.736

rs7004381
Position: chr8:42,551,161 (Open in UCSC Genome Browser)
Distance to lead SNP: 663 bp
Distance to nearest TSS: 143,409 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=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.788

rs1530847
Position: chr8:42,548,239 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,259 bp
Distance to nearest TSS: 140,487 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=0.811 / CHB: D'=1.0, r2=0.933 / JPT: D'=1.0, r2=1.0

rs10958725
Position: chr8:42,524,584 (Open in UCSC Genome Browser)
Distance to lead SNP: 25,914 bp
Distance to nearest TSS: 116,832 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=0.932 / CHB: D'=0.923, r2=0.699 / JPT: D'=1.0, r2=0.829 / YRI: D'=1.0, r2=0.725

rs6990603
Position: chr8:42,523,039 (Open in UCSC Genome Browser)
Distance to lead SNP: 27,459 bp
Distance to nearest TSS: 115,287 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=0.879 / CHB: D'=1.0, r2=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.953, r2=0.663

rs6997909
Position: chr8:42,560,249 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,751 bp
Distance to nearest TSS: 152,497 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=0.933 / JPT: D'=1.0, r2=1.0

rs13273442
Position: chr8:42,544,017 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,481 bp
Distance to nearest TSS: 136,265 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=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.788

rs1451240
Position: chr8:42,546,711 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,787 bp
Distance to nearest TSS: 138,959 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=0.938 / CHB: D'=1.0, r2=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs4236926
Position: chr8:42,578,059 (Open in UCSC Genome Browser)
Distance to lead SNP: 27,561 bp
Distance to nearest TSS: 13,703 bp
GENCODE v7 location: Intron
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.919, r2=0.845 / CHB: D'=0.909, r2=0.758 / JPT: D'=1.0, r2=1.0

rs1979140
Position: chr8:42,530,836 (Open in UCSC Genome Browser)
Distance to lead SNP: 19,662 bp
Distance to nearest TSS: 123,084 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=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.953, r2=0.686

rs10958726
Position: chr8:42,535,909 (Open in UCSC Genome Browser)
Distance to lead SNP: 14,589 bp
Distance to nearest TSS: 128,157 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=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.955, r2=0.747

rs6474415
Position: chr8:42,562,938 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,440 bp
Distance to nearest TSS: 155,186 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=0.933 / JPT: D'=1.0, r2=1.0

rs6474414
Position: chr8:42,560,336 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,838 bp
Distance to nearest TSS: 152,584 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=0.933 / JPT: D'=1.0, r2=1.0

rs4736835
Position: chr8:42,547,033 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,465 bp
Distance to nearest TSS: 139,281 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=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs16891561
Position: chr8:42,579,739 (Open in UCSC Genome Browser)
Distance to lead SNP: 29,241 bp
Distance to nearest TSS: 12,023 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.938, r2=0.879 / CHB: D'=0.929, r2=0.808 / JPT: D'=1.0, r2=1.0

rs5005909
Position: chr8:42,528,667 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,831 bp
Distance to nearest TSS: 120,915 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.873 / CHB: D'=0.925, r2=0.704 / JPT: D'=1.0, r2=0.885 / YRI: D'=0.951, r2=0.863

rs1451239
Position: chr8:42,546,542 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,956 bp
Distance to nearest TSS: 138,790 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.938 / CHB: D'=0.913, r2=0.667 / JPT: D'=1.0, r2=1.0

rs7837296
Position: chr8:42,526,894 (Open in UCSC Genome Browser)
Distance to lead SNP: 23,604 bp
Distance to nearest TSS: 119,142 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.879 / CHB: D'=1.0, r2=0.93 / JPT: D'=1.0, r2=1.0

rs1955185
Position: chr8:42,549,647 (Open in UCSC Genome Browser)
Distance to lead SNP: 851 bp
Distance to nearest TSS: 141,895 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=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.736

rs7842601
Position: chr8:42,537,055 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,443 bp
Distance to nearest TSS: 129,303 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=0.933 / JPT: D'=1.0, r2=1.0 / YRI: D'=0.955, r2=0.747




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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