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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rs1847461

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: 8 x 10-06
Odds ratio [95% confidence interval]: 1.80 [NR]
Gene: MRPL2P1 - C12orf12
Minor allele frequency (controls): 0.94

Lead SNP

rs1847461
Position: chr12:91,077,508 (Open in UCSC Genome Browser)
Distance to nearest TSS: 929,578 bp
GENCODE v7 location: Intergenic region
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:

rs11105747
Position: chr12:91,073,629 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,879 bp
Distance to nearest TSS: 925,699 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=0.895

rs10859021
Position: chr12:91,073,518 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,990 bp
Distance to nearest TSS: 925,588 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=0.819

rs11105751
Position: chr12:91,082,817 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,309 bp
Distance to nearest TSS: 934,887 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=0.895

rs12368019
Position: chr12:91,083,885 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,377 bp
Distance to nearest TSS: 935,955 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=0.895 / YRI: D'=1.0, r2=0.736

rs10859018
Position: chr12:91,068,508 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,000 bp
Distance to nearest TSS: 920,578 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 / YRI: D'=0.845, r2=0.618

rs10859022
Position: chr12:91,074,224 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,284 bp
Distance to nearest TSS: 926,294 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=0.895

rs10859036
Position: chr12:91,107,363 (Open in UCSC Genome Browser)
Distance to lead SNP: 29,855 bp
Distance to nearest TSS: 959,433 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=0.895 / YRI: D'=1.0, r2=0.607

rs17250987
Position: chr12:91,080,025 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,517 bp
Distance to nearest TSS: 932,095 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=0.864

rs11105758
Position: chr12:91,091,591 (Open in UCSC Genome Browser)
Distance to lead SNP: 14,083 bp
Distance to nearest TSS: 943,661 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=0.864 / YRI: D'=1.0, r2=0.653

rs11105762
Position: chr12:91,099,550 (Open in UCSC Genome Browser)
Distance to lead SNP: 22,042 bp
Distance to nearest TSS: 951,620 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=0.895

rs10859017
Position: chr12:91,065,648 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,860 bp
Distance to nearest TSS: 917,718 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=0.895

rs10859020
Position: chr12:91,068,976 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,532 bp
Distance to nearest TSS: 921,046 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=0.893

rs10859023
Position: chr12:91,075,451 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,057 bp
Distance to nearest TSS: 927,521 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=0.865

rs1504149
Position: chr12:91,100,420 (Open in UCSC Genome Browser)
Distance to lead SNP: 22,912 bp
Distance to nearest TSS: 952,490 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=0.895

rs1504150
Position: chr12:91,100,439 (Open in UCSC Genome Browser)
Distance to lead SNP: 22,931 bp
Distance to nearest TSS: 952,509 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=0.895 / YRI: D'=1.0, r2=0.607

rs10859031
Position: chr12:91,097,040 (Open in UCSC Genome Browser)
Distance to lead SNP: 19,532 bp
Distance to nearest TSS: 949,110 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=0.871 / YRI: D'=1.0, r2=0.7

rs10859032
Position: chr12:91,097,225 (Open in UCSC Genome Browser)
Distance to lead SNP: 19,717 bp
Distance to nearest TSS: 949,295 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=0.895

rs10859035
Position: chr12:91,107,032 (Open in UCSC Genome Browser)
Distance to lead SNP: 29,524 bp
Distance to nearest TSS: 959,102 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=0.895 / YRI: D'=1.0, r2=0.607

rs12372205
Position: chr12:91,091,399 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,891 bp
Distance to nearest TSS: 943,469 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=0.895

rs12367136
Position: chr12:91,082,292 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,784 bp
Distance to nearest TSS: 934,362 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=0.84

rs11105737
Position: chr12:91,059,729 (Open in UCSC Genome Browser)
Distance to lead SNP: 17,779 bp
Distance to nearest TSS: 911,799 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=0.895

rs17837047
Position: chr12:91,089,889 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,381 bp
Distance to nearest TSS: 941,959 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=0.895 / YRI: D'=1.0, r2=0.607

rs11105743
Position: chr12:91,069,397 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,111 bp
Distance to nearest TSS: 921,467 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=0.893

rs10859027
Position: chr12:91,088,874 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,366 bp
Distance to nearest TSS: 940,944 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=0.895 / YRI: D'=1.0, r2=0.7

rs11105745
Position: chr12:91,070,867 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,641 bp
Distance to nearest TSS: 922,937 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=0.887 / YRI: D'=0.845, r2=0.619

rs11105748
Position: chr12:91,076,730 (Open in UCSC Genome Browser)
Distance to lead SNP: 778 bp
Distance to nearest TSS: 928,800 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=0.844 / YRI: D'=1.0, r2=0.736

rs11105742
Position: chr12:91,068,209 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,299 bp
Distance to nearest TSS: 920,279 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=0.895

rs11105750
Position: chr12:91,077,041 (Open in UCSC Genome Browser)
Distance to lead SNP: 467 bp
Distance to nearest TSS: 929,111 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=0.895 / YRI: D'=1.0, r2=0.736

rs11105753
Position: chr12:91,085,090 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,582 bp
Distance to nearest TSS: 937,160 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=1.0

rs11105757
Position: chr12:91,091,255 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,747 bp
Distance to nearest TSS: 943,325 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=0.895

rs11105744
Position: chr12:91,070,405 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,103 bp
Distance to nearest TSS: 922,475 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'=0.875, r2=0.766

rs17250924
Position: chr12:91,061,042 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,466 bp
Distance to nearest TSS: 913,112 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'=0.942, r2=0.839

rs11105746
Position: chr12:91,071,028 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,480 bp
Distance to nearest TSS: 923,098 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=0.893 / YRI: D'=0.845, r2=0.619

rs17837048
Position: chr12:91,090,020 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,512 bp
Distance to nearest TSS: 942,090 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=0.895 / YRI: D'=1.0, r2=0.736

rs12372394
Position: chr12:91,079,296 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,788 bp
Distance to nearest TSS: 931,366 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'=0.939, r2=0.788 / YRI: D'=1.0, r2=0.735

rs10859029
Position: chr12:91,090,368 (Open in UCSC Genome Browser)
Distance to lead SNP: 12,860 bp
Distance to nearest TSS: 942,438 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=0.895 / YRI: D'=1.0, r2=0.607




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 01:19:21
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