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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rs17135859

Associations

Study: Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients. [PMID:21326311]
First author: Bhatnagar P
Journal: J Hum Genet
Date: 02/17/2011
Phenotype: F-cell distribution
Study population: 440 African ancestry individuals
Association P-value: 8 x 10-06
Odds ratio [95% confidence interval]: .97 [0.54-1.40] unit increase
Gene: YTHDC2 - KCNN2
Risk allele: C
Minor allele frequency (controls): 0.19

Lead SNP

rs17135859
Position: chr5:112,996,654 (Open in UCSC Genome Browser)
Distance to nearest TSS: 396,218 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:

rs6867579
Position: chr5:112,899,573 (Open in UCSC Genome Browser)
Distance to lead SNP: 97,081 bp
Distance to nearest TSS: 29,508 bp
GENCODE v7 location: Coding region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.931, r2=0.812 / CHB: D'=1.0, r2=0.551

rs7707681
Position: chr5:112,996,226 (Open in UCSC Genome Browser)
Distance to lead SNP: 428 bp
Distance to nearest TSS: 396,646 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

rs7706721
Position: chr5:112,825,706 (Open in UCSC Genome Browser)
Distance to lead SNP: 170,948 bp
Distance to nearest TSS: 3,952 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 5b - DNaseI-seq peak (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.931, r2=0.812 / CHB: D'=1.0, r2=0.551

rs13435951
Position: chr5:112,994,003 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,651 bp
Distance to nearest TSS: 398,869 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

rs2115211
Position: chr5:112,966,039 (Open in UCSC Genome Browser)
Distance to lead SNP: 30,615 bp
Distance to nearest TSS: 426,833 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=0.93 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs2162844
Position: chr5:112,988,892 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,762 bp
Distance to nearest TSS: 403,980 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=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs6594742
Position: chr5:112,982,681 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,973 bp
Distance to nearest TSS: 410,191 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=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs4705465
Position: chr5:112,993,624 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,030 bp
Distance to nearest TSS: 399,248 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

rs2416324
Position: chr5:113,009,791 (Open in UCSC Genome Browser)
Distance to lead SNP: 13,137 bp
Distance to nearest TSS: 383,081 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

rs6889326
Position: chr5:112,965,108 (Open in UCSC Genome Browser)
Distance to lead SNP: 31,546 bp
Distance to nearest TSS: 427,764 bp
GENCODE v7 location: Intergenic region
RegulomeDB Score: 6 - Motif (Open in RegulomeDB)
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.932, r2=0.869

rs4705464
Position: chr5:112,993,214 (Open in UCSC Genome Browser)
Distance to lead SNP: 3,440 bp
Distance to nearest TSS: 399,658 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs13170795
Position: chr5:112,974,969 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,685 bp
Distance to nearest TSS: 417,903 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs6891156
Position: chr5:112,960,124 (Open in UCSC Genome Browser)
Distance to lead SNP: 36,530 bp
Distance to nearest TSS: 432,748 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.932, r2=0.869

rs6881949
Position: chr5:112,974,340 (Open in UCSC Genome Browser)
Distance to lead SNP: 22,314 bp
Distance to nearest TSS: 418,532 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.93 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs7709362
Position: chr5:112,990,998 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,656 bp
Distance to nearest TSS: 401,874 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=1.0

rs6594741
Position: chr5:112,982,650 (Open in UCSC Genome Browser)
Distance to lead SNP: 14,004 bp
Distance to nearest TSS: 410,222 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs2416322
Position: chr5:112,966,663 (Open in UCSC Genome Browser)
Distance to lead SNP: 29,991 bp
Distance to nearest TSS: 426,209 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs4283775
Position: chr5:112,963,314 (Open in UCSC Genome Browser)
Distance to lead SNP: 33,340 bp
Distance to nearest TSS: 429,558 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.93 / CHB: D'=1.0, r2=1.0

rs6889348
Position: chr5:112,965,145 (Open in UCSC Genome Browser)
Distance to lead SNP: 31,509 bp
Distance to nearest TSS: 427,727 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.932, r2=0.869

rs12189067
Position: chr5:112,981,528 (Open in UCSC Genome Browser)
Distance to lead SNP: 15,126 bp
Distance to nearest TSS: 411,344 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs17333665
Position: chr5:112,970,602 (Open in UCSC Genome Browser)
Distance to lead SNP: 26,052 bp
Distance to nearest TSS: 422,270 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs2195374
Position: chr5:112,998,733 (Open in UCSC Genome Browser)
Distance to lead SNP: 2,079 bp
Distance to nearest TSS: 394,139 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

rs2162845
Position: chr5:112,988,870 (Open in UCSC Genome Browser)
Distance to lead SNP: 7,784 bp
Distance to nearest TSS: 404,002 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs13183014
Position: chr5:112,964,664 (Open in UCSC Genome Browser)
Distance to lead SNP: 31,990 bp
Distance to nearest TSS: 428,208 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=0.79 / JPT: D'=1.0, r2=1.0

rs13180357
Position: chr5:112,969,041 (Open in UCSC Genome Browser)
Distance to lead SNP: 27,613 bp
Distance to nearest TSS: 423,831 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs6872020
Position: chr5:112,960,035 (Open in UCSC Genome Browser)
Distance to lead SNP: 36,619 bp
Distance to nearest TSS: 432,837 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.933 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs13182972
Position: chr5:112,904,402 (Open in UCSC Genome Browser)
Distance to lead SNP: 92,252 bp
Distance to nearest TSS: 24,679 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=0.931, r2=0.812 / CHB: D'=1.0, r2=0.551




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
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