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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rs12073837

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: 2 x 10-06
Odds ratio [95% confidence interval]: 1.39 [0.82-1.96] unit increase
Gene: LOC100129376
Risk allele: T
Minor allele frequency (controls): 0.19

Lead SNP

rs12073837
Position: chr1:221,010,205 (Open in UCSC Genome Browser)
Distance to nearest TSS: 47,842 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:

rs11118616
Position: chr1:221,005,656 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,549 bp
Distance to nearest TSS: 6,420 bp
GENCODE v7 location: Exon, non-coding
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.902 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.705

rs1494368
Position: chr1:221,004,168 (Open in UCSC Genome Browser)
Distance to lead SNP: 6,037 bp
Distance to nearest TSS: 4,932 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=1.0 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.802

rs17596850
Position: chr1:220,992,343 (Open in UCSC Genome Browser)
Distance to lead SNP: 17,862 bp
Distance to nearest TSS: 6,893 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=0.948 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs17650107
Position: chr1:220,986,546 (Open in UCSC Genome Browser)
Distance to lead SNP: 23,659 bp
Distance to nearest TSS: 29,019 bp
GENCODE v7 location: Intron
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=0.947 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs903319
Position: chr1:220,985,811 (Open in UCSC Genome Browser)
Distance to lead SNP: 24,394 bp
Distance to nearest TSS: 28,284 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=0.948 / CHB: D'=1.0, r2=0.946 / JPT: D'=1.0, r2=1.0

rs881995
Position: chr1:220,984,494 (Open in UCSC Genome Browser)
Distance to lead SNP: 25,711 bp
Distance to nearest TSS: 26,967 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=0.947 / CHB: D'=1.0, r2=0.893 / JPT: D'=1.0, r2=1.0

rs12145674
Position: chr1:221,000,273 (Open in UCSC Genome Browser)
Distance to lead SNP: 9,932 bp
Distance to nearest TSS: 5,499 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=0.948 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs2378425
Position: chr1:221,016,058 (Open in UCSC Genome Browser)
Distance to lead SNP: 5,853 bp
Distance to nearest TSS: 41,989 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=0.944 / CHB: D'=1.0, r2=0.945 / JPT: D'=1.0, r2=1.0 / YRI: D'=1.0, r2=0.816

rs2279638
Position: chr1:221,001,787 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,418 bp
Distance to nearest TSS: 3,985 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 / YRI: D'=1.0, r2=0.762

rs7553447
Position: chr1:220,989,534 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,671 bp
Distance to nearest TSS: 9,702 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

rs1335919
Position: chr1:221,018,385 (Open in UCSC Genome Browser)
Distance to lead SNP: 8,180 bp
Distance to nearest TSS: 39,662 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=0.907

rs11118609
Position: chr1:220,988,490 (Open in UCSC Genome Browser)
Distance to lead SNP: 21,715 bp
Distance to nearest TSS: 10,746 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

rs7544735
Position: chr1:220,998,913 (Open in UCSC Genome Browser)
Distance to lead SNP: 11,292 bp
Distance to nearest TSS: 11,177 bp
GENCODE v7 location: Intergenic region
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.948 / CHB: D'=1.0, r2=1.0 / JPT: D'=1.0, r2=1.0

rs17008806
Position: chr1:220,976,257 (Open in UCSC Genome Browser)
Distance to lead SNP: 33,948 bp
Distance to nearest TSS: 18,730 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.948 / CHB: D'=1.0, r2=0.946 / JPT: D'=1.0, r2=0.951

rs10495152
Position: chr1:220,990,355 (Open in UCSC Genome Browser)
Distance to lead SNP: 19,850 bp
Distance to nearest TSS: 8,881 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

rs1494372
Position: chr1:221,014,621 (Open in UCSC Genome Browser)
Distance to lead SNP: 4,416 bp
Distance to nearest TSS: 43,426 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=0.907

rs7530074
Position: chr1:220,989,266 (Open in UCSC Genome Browser)
Distance to lead SNP: 20,939 bp
Distance to nearest TSS: 9,970 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

rs984676
Position: chr1:221,008,422 (Open in UCSC Genome Browser)
Distance to lead SNP: 1,783 bp
Distance to nearest TSS: 49,625 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

rs12129004
Position: chr1:220,985,515 (Open in UCSC Genome Browser)
Distance to lead SNP: 24,690 bp
Distance to nearest TSS: 27,988 bp
GENCODE v7 location: Intron
No regulatory annotation found
Linkage disequilibrium with Lead SNP (HapMap 2): CEU: D'=1.0, r2=0.88 / CHB: D'=1.0, r2=0.711 / JPT: D'=1.0, r2=0.766




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 01:19:11
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