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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rs11209026

Associations

Study: Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility. [PMID:21743469]
First author: Evans DM
Journal: Nat Genet
Date: 07/10/2011
Phenotype: Ankylosing spondylitis
Study population: 3,023 European ancestry cases, 8,779 European ancestry controls
Replication population: 2,111 European ancestry cases, 4,483 European ancestry controls
Association P-value: 2 x 10-17
Gene: IL23R
Risk allele: G
Minor allele frequency (controls): 0.93

Study: Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. [PMID:21297633]
First author: Anderson CA
Journal: Nat Genet
Date: 02/06/2011
Phenotype: Ulcerative colitis
Study population: 6,687 European ancestry cases, 19,718 European ancestry controls
Replication population: 9,628 European ancestry cases, 12,917 European ancestry controls
Association P-value: 5 x 10-28
Odds ratio [95% confidence interval]: 1.74 [1.57-1.92]
Gene: IL23R
Risk allele: G
Minor allele frequency (controls): 0.94

Study: Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. [PMID:21102463]
First author: Franke A
Journal: Nat Genet
Date: 11/21/2010
Phenotype: Crohn's disease
Study population: 6,333 European descent cases, 15,056 European descent controls
Replication population: 15,694 European descent cases, 14,026 European descent controls, 414 European descent parent-offspring trios
Association P-value: 1 x 10-64
Odds ratio [95% confidence interval]: 2.66 [2.36-3.00]
Gene: IL23R
Risk allele: G
Minor allele frequency (controls): 0.93

Study: A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. [PMID:20953190]
First author: Strange A
Journal: Nat Genet
Date: 10/17/2010
Phenotype: Psoriasis
Study population: 2,178 European ancestry cases, 5,175 European ancestry controls
Replication population: 3,174 European ancestry cases, 5,464 European ancestry controls
Association P-value: 7 x 10-07
Odds ratio [95% confidence interval]: 1.49 [1.27-1.74]
Gene: IL23R

Study: Genome-wide association study of ankylosing spondylitis identifies non-MHC susceptibility loci. [PMID:20062062]
First author: Reveille JD
Journal: Nat Genet
Date: 01/10/2010
Phenotype: Ankylosing spondylitis
Study population: 2,053 European descent cases, 5,140 European descent controls
Replication population: 898 British cases, 1,518 British controls
Association P-value: 9 x 10-14
Odds ratio [95% confidence interval]: 1.89 [1.56-2.27]
Gene: IL23R
Minor allele frequency (controls): 0.94

Study: Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. [PMID:19915572]
First author: Barrett JC
Journal: Nat Genet
Date: 11/15/2009
Phenotype: Ulcerative colitis
Study population: 2,361 European ancestry cases, 5,417 European ancestry controls
Replication population: 2,321 European ancestry cases, 4,818 European ancestry controls
Association P-value: 3 x 10-10
Gene: IL23R

Study: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. [PMID:19122664]
First author: Silverberg MS
Journal: Nat Genet
Date: 01/04/2009
Phenotype: Ulcerative colitis
Study population: 1,022 cases, 2,503 controls
Replication population: 1,387 cases, 1,115 controls
Association P-value: 1 x 10-08
Odds ratio [95% confidence interval]: 1.79
Gene: IL23R
Minor allele frequency (controls): 0.93

Study: Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. [PMID:18758464]
First author: Kugathasan S
Journal: Nat Genet
Date: 08/31/2008
Phenotype: Inflammatory bowel disease
Study population: 1,011 cases,4,250 controls
Replication population: 1,922 cases,14,124 controls
Association P-value: 7 x 10-11
Odds ratio [95% confidence interval]: 2.56 [1.92-3.45]
Gene: IL23R
Minor allele frequency (controls): 0.94

Study: Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. [PMID:17447842]
First author: Libioulle C
Journal: PLoS Genet
Date: 03/05/2007
Phenotype: Crohn's disease
Study population: 547 cases,928 controls
Replication population: 1,266 cases,559 controls,428 trios
Association P-value: 2 x 10-18
Odds ratio [95% confidence interval]: 2.92 [NR]
Gene: IL23R
Minor allele frequency (controls): 0.92

Study: A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. [PMID:17068223]
First author: Duerr RH
Journal: Science
Date: 10/26/2006
Phenotype: Inflammatory bowel disease
Study population: 547 cases,548 controls
Replication population: 401 cases,433 controls,883 families,1,119 affected offspring
Association P-value: 4 x 10-11
Odds ratio [95% confidence interval]: 3.84 [2.33-6.66]
Gene: IL23R
Risk allele: G
Minor allele frequency (controls): 0.93

Lead SNP

rs11209026
Position: chr1:67,705,958 (Open in UCSC Genome Browser)
Distance to nearest TSS: 15,588 bp
GENCODE v7 location: Coding 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 

No SNPs found for this LD threshold.




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 01:19:10
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