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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rs4636294

Associations

Study: Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi. [PMID:19578365]
First author: Falchi M
Journal: Nat Genet
Date: 07/05/2009
Phenotype: Cutaneous nevi
Study population: 1,524 European twins
Replication population: 4,107 European individuals
Association P-value: 3 x 10-15
Odds ratio [95% confidence interval]: .20 [0.13-0.27] increase in log nevus count
Gene: IFNE - MTAP
Risk allele: A
Minor allele frequency (controls): 0.48

Lead SNP

rs4636294
Position: chr9:21,747,803 (Open in UCSC Genome Browser)
Distance to nearest TSS: 188,134 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:

rs2043991
Position: chr9:21,731,081 (Open in UCSC Genome Browser)
Distance to lead SNP: 16,722 bp
Distance to nearest TSS: 171,412 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 2b - ChIP-seq peak + any 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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.857

rs10116451
Position: chr9:21,727,352 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,451 bp
Distance to nearest TSS: 167,683 bp
GENCODE v7 location: Intergenic region
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=0.945 / JPT: D'=1.0, r2=0.855 / YRI: D'=1.0, r2=0.857

rs9298823
Position: chr9:21,749,607 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,804 bp
Distance to nearest TSS: 189,938 bp
GENCODE v7 location: Intergenic region
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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.931

rs4341236
Position: chr9:21,727,208 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,595 bp
Distance to nearest TSS: 167,539 bp
GENCODE v7 location: Intergenic region
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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.857

rs1561652
Position: chr9:21,742,816 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,987 bp
Distance to nearest TSS: 183,147 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=0.841 / JPT: D'=0.946, r2=0.851 / YRI: D'=1.0, r2=1.0

rs1414242
Position: chr9:21,748,239 (Open in UCSC Genome Browser)
Distance to lead SNP: 436 bp
Distance to nearest TSS: 188,570 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=0.924 / CHB: D'=1.0, r2=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=1.0

rs1414244
Position: chr9:21,748,532 (Open in UCSC Genome Browser)
Distance to lead SNP: 729 bp
Distance to nearest TSS: 188,863 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.931

rs1414245
Position: chr9:21,750,069 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,266 bp
Distance to nearest TSS: 190,400 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.931

rs1414247
Position: chr9:21,750,170 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,367 bp
Distance to nearest TSS: 190,501 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.931

rs1414257
Position: chr9:21,757,767 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,964 bp
Distance to nearest TSS: 198,098 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=0.945 / JPT: D'=0.946, r2=0.851 / YRI: D'=1.0, r2=0.928

rs4548267
Position: chr9:21,748,073 (Open in UCSC Genome Browser)
Distance to lead SNP: 270 bp
Distance to nearest TSS: 188,404 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=0.941 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=1.0

rs1335505
Position: chr9:21,748,484 (Open in UCSC Genome Browser)
Distance to lead SNP: 681 bp
Distance to nearest TSS: 188,815 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.931

rs1335506
Position: chr9:21,750,267 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,464 bp
Distance to nearest TSS: 190,598 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.931

rs1335507
Position: chr9:21,750,445 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,642 bp
Distance to nearest TSS: 190,776 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.931

rs1335508
Position: chr9:21,750,587 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,784 bp
Distance to nearest TSS: 190,918 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.931

rs7874319
Position: chr9:21,735,881 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,922 bp
Distance to nearest TSS: 176,212 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=0.882 / CHB: D'=1.0, r2=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.857

rs1414235
Position: chr9:21,726,306 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,497 bp
Distance to nearest TSS: 166,637 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=0.942 / JPT: D'=1.0, r2=0.851 / YRI: D'=1.0, r2=0.857

rs1414237
Position: chr9:21,732,912 (Open in UCSC Genome Browser)
Distance to lead SNP: 14,891 bp
Distance to nearest TSS: 173,243 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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.857

rs1414238
Position: chr9:21,737,149 (Open in UCSC Genome Browser)
Distance to lead SNP: 10,654 bp
Distance to nearest TSS: 177,480 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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.857

rs1414248
Position: chr9:21,750,884 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,081 bp
Distance to nearest TSS: 191,215 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.931

rs10757238
Position: chr9:21,732,466 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,337 bp
Distance to nearest TSS: 172,797 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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.857

rs2027163
Position: chr9:21,738,133 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,670 bp
Distance to nearest TSS: 178,464 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=0.944 / JPT: D'=1.0, r2=0.881 / YRI: D'=1.0, r2=0.813

rs1335502
Position: chr9:21,736,274 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,529 bp
Distance to nearest TSS: 176,605 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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.856

rs9695494
Position: chr9:21,727,799 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,004 bp
Distance to nearest TSS: 168,130 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=0.945 / JPT: D'=1.0, r2=0.857 / YRI: D'=1.0, r2=0.856

rs2119467
Position: chr9:21,746,107 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,696 bp
Distance to nearest TSS: 186,438 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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=1.0

rs6475566
Position: chr9:21,733,500 (Open in UCSC Genome Browser)
Distance to lead SNP: 14,303 bp
Distance to nearest TSS: 173,831 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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.857

rs7854990
Position: chr9:21,725,962 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,841 bp
Distance to nearest TSS: 166,293 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=0.945 / JPT: D'=1.0, r2=0.857 / YRI: D'=1.0, r2=0.857

rs2891159
Position: chr9:21,747,672 (Open in UCSC Genome Browser)
Distance to lead SNP: 131 bp
Distance to nearest TSS: 188,003 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=1.0

rs2891166
Position: chr9:21,726,819 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,984 bp
Distance to nearest TSS: 167,150 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=0.891 / JPT: D'=1.0, r2=0.816 / YRI: D'=1.0, r2=0.857

rs4352937
Position: chr9:21,747,749 (Open in UCSC Genome Browser)
Distance to lead SNP: 54 bp
Distance to nearest TSS: 188,080 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=1.0

rs7846943
Position: chr9:21,720,108 (Open in UCSC Genome Browser)
Distance to lead SNP: 27,695 bp
Distance to nearest TSS: 160,439 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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.828

rs10757237
Position: chr9:21,727,369 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,434 bp
Distance to nearest TSS: 167,700 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=0.945 / JPT: D'=1.0, r2=0.857 / YRI: D'=1.0, r2=0.856

rs10757240
Position: chr9:21,734,449 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,354 bp
Distance to nearest TSS: 174,780 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=0.849 / YRI: D'=1.0, r2=0.855

rs10757242
Position: chr9:21,739,592 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,211 bp
Distance to nearest TSS: 179,923 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=0.857

rs1832076
Position: chr9:21,726,664 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,139 bp
Distance to nearest TSS: 166,995 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=0.945 / JPT: D'=1.0, r2=0.86 / YRI: D'=1.0, r2=0.857

rs10811605
Position: chr9:21,738,444 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,359 bp
Distance to nearest TSS: 178,775 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=0.937 / JPT: D'=0.939, r2=0.832 / YRI: D'=1.0, r2=0.8

rs2119466
Position: chr9:21,745,990 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,813 bp
Distance to nearest TSS: 186,321 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=1.0

rs7852900
Position: chr9:21,746,796 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,007 bp
Distance to nearest TSS: 187,127 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=0.929 / JPT: D'=1.0, r2=0.882 / YRI: D'=1.0, r2=1.0

rs1372057
Position: chr9:21,747,110 (Open in UCSC Genome Browser)
Distance to lead SNP: 693 bp
Distance to nearest TSS: 187,441 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: D'=1.0, r2=1.0

rs10738597
Position: chr9:21,746,396 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,407 bp
Distance to nearest TSS: 186,727 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=0.945 / JPT: D'=1.0, r2=0.904 / YRI: 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 01:19:19
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