Overview

Meta-analysis of six ulcerative colitis (UC) disease genome wide association studies (GWAS) comprising 6,687 affected individuals (cases) and 19,718 controls of European descent. Genotyping in the six studies was performed on Illumina Hap370 or 610-Quad platforms. Imputation was carried out using the IMPUTE software.  In total, 50 SNPs were selected for follow-up in 9,628 cases and 12,917 controls.  This identified 29 new risk loci, bringing the total of ulcerative colitis associated loci to 47 (note - 2 previously identified loci do not meet genome-wide significance in this study).

Study Type
Whole Genome Association Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryUC668719718--
ReplicationUC962812917--
Exclusion Criteria

Any individuls or samples with <10% missing data were removed.

Duplicate samples across cohorts were identified and the sample with the lowest call rate was removed.

Hardy-Weinberg equilibrium (HWE) P<10-4

For eQTL Analysis, SNPs were excluded as below:-

  • Minor allele frequency < 5%
  • Call rate < 95%
  • Hardy-Weinbery equilibrium (HWE) P<10-3

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p31.3chr1:67128876-67302310IL23R  rs11209026G > A0.0655.12e-28D1.75 (1.56-1.92)D
1p36.12chr1:22326008-22411939rs7524102A > G0.1721.65e-13C 
1p36.13chr1:19821756-19953230rs6426833A > G0.4593.93e-35D1.3 (1.25-1.35)D
1p36.23chr1:7853370-8140630UTS2  PARK7  TNFRSF9  ERRFI1  rs35675666G > T0.1714.84e-09C 
1p36.32chr1:2431888-2879054TNFRSF14  FAM213B  PLCH2  MMEL1  rs734999C > T0.4763.34e-09C 
1q23.3chr1:161419627-161668253FCGR2B  FCGR2A  HSPA6  rs1801274A > G0.4952.16e-20D1.2 (1.16-1.27)D
1q32.1chr1:206709013-206867232IL19  IL10  rs3024505G > A0.1595.76e-17D1.25 (1.19-1.32)D
1q32.1chr1:200892467-201069559C1orf106  rs7554511C > A0.2792.04e-13D 
2p16.1chr2:60706158-61642429PUS10  rs7608910A > G0.3901.70e-14D1.19 (1.14-1.24)D
2q11.2chr2:101678428-102080305IL1R2  rs2310173G > T0.4613.17e-12C 
2q35chr2:218018463-218377795ARPC2  SLC11A1  AAMP  CXCR1  CXCR2  rs11676348C > T0.4861.25e-10C 
2q37.3chr2:240621671-240716127GPR35  rs4676406T > G0.4848.32e-11D1.14 (1.09-1.18)D
3p21.31chr3:48456895-50711580MST1  BSN  AMIGO3  APEH  UBA7  GMPPB  rs9822268G > A0.3021.60e-17D1.21 (1.16-1.26)D
4q27chr4:122041392-122644147IL21  ADAD1  IL2  rs17388568G > A0.2739.49e-07D1.12 (1.07-1.17)D
5p13.1chr5:40286865-40626651PTGER4  rs6451493T > G0.3902.80e-09C 
5p13.2chr5:35795636-36035028IL7R  rs3194051A > G0.2694.22e-08C 
5p15.2chr5:10667329-10839728DAP  rs267939T > C0.3686.01e-12C 
5p15.33chr5:490122-717906EXOC3  rs11739663T > C0.2332.80e-08D1.15 (1.09-1.2)D
5q31.1chr5:135044841-135190861rs254560G > A0.3971.25e-09C 
5q33.3chr5:159397971-159460964IL12B  rs6871626C > A0.3341.11e-21C 
6p21.1chr6:43803265-43855043rs943072T > G0.0922.37e-10C 
6q21chr6:105959511-106115679PRDM1  rs6911490C > T0.2101.01e-08C 
6q23.3chr6:137568592-137806067rs6920220G > A0.2078.05e-17C 
7p22.3chr7:2695130-2891602GNA12  rs798502A > C0.2892.61e-15C 
7q31.1chr7:107834421-107964373rs4510766A > G0.4412.00e-16D1.2 (1.15-1.27)D
7q32.1chr7:128911686-129137466TNPO3  IRF5  rs4728142G > A0.4441.74e-08C 
9p24.1chr9:4944089-5274545JAK2  rs10758669A > C0.3502.22e-25C 
9q32chr9:114715997-114937465TNFSF15  TNFSF8  rs4246905C > T0.2875.65e-12C 
9q34.3chr9:136243135-136514725SDCCAG3  SEC16A  INPP5E  CARD9  SNAPC4  rs10781499G > A0.4112.62e-19C 
10p11.21chr10:34896568-35623424CCNY  rs12261843T > G0.2867.09e-10C 
10q24.2chr10:99508770-99570210rs6584283C > T0.4728.46e-21D1.21 (1.16-1.26)D
11p15.5chr11:1845142-1946041LSP1  rs907611G > A0.3171.38e-10C 
11q13.5chr11:76324636-76632292rs2155219T > G0.5005.39e-16C 
11q23.2chr11:114388931-114716152rs678170A > G0.3394.65e-14C 
12q15chr12:68036752-68116292IFNG  IL26  rs7134599G > A0.3851.06e-16D1.19 (1.14-1.24)D
13q12.13chr13:26932960-26990142rs17085007T > C0.1789.65e-17C 
13q14.11chr13:40435146-40471356rs941823C > T0.2443.82e-12C 
16q22.1chr16:68397853-68808992ZFP90  rs6499188A > G0.2513.97e-08D1.14 (1.09-1.2)D
16q24.1chr16:85950449-85990498rs16940202T > C0.1805.96e-19C 
17q12chr17:39226421-40083963PNMT  IKZF3  GSDMB  ORMDL3  ZPBP2  rs2872507G > A0.4635.44e-11D1.15 (1.10-1.19)D
20q13.12chr20:44430797-44508282SERINC3  rs6017342C > A0.4621.09e-20D1.2 (1.15-1.27)D
20q13.33chr20:63564900-63795414TNFRSF6B  RTEL1  STMN3  ZBTB46  ZGPAT  SLC2A4RG  rs2297441A > G0.2341.70e-10C 
21q21.1chr21:15326120-15470979rs1297265A > G0.4366.99e-13C 
21q22.2chr21:39081110-39111851rs2836878G > A0.2621.86e-22D1.25 (1.2-1.32)D
21q22.3chr21:44145591-44263692ICOSLG  CH507-9B2.1  rs2838519A > G0.3906.41e-11C 
22q13.33chr22:49927295-50052284PIM3  IL17REL  rs5771069G > A0.4851.87e-07D1.11 (1.08-1.16)D
MHCchr6:32371299-32684804HLA-DQA2  HLA-DRB1  BTNL2  HLA-DRB5  HLA-DQA1  HLA-DRA  rs9268853T > C0.3391.35e-55D1.41 (1.33-1.47)D

Criteria

GDXHsS00029 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date