Overview

A genome-wide association study meta-analysis of 4,533 individuals with celiac disease (cases) and 10,750 controls of European descent. Genotyping of the studies were performed on Illumina Infinium HumanHap300 beadchip. A further 231,362 additional non-HLA markers from Illumina Hap550 marker set were tested for association in 3,796 cases and 8,154 controls. Genotype imputation using BEAGLE software and HapMap3 reference samples for samples typed on HumanHap300 chip was performed. After QC SNPs from 113 loci were selected for replication in 4,918 cases and 5,684 controls. All tests for association were conducted using PLINK v1.07 allowing the discovery of 13 novel celiac disease susceptibility loci.

Study Type
Whole Genome Association Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryCELNULL453310750--
ReplicationCELNULL49185684--
Exclusion Criteria

SNPs

  • Call rate >95%.
  • HWE (P<0.0001).
  • Manual checking of discovery SNP signal clouds for artefacts.

Sample

  • Call rate >98%
  • Non-european descent via EIGENSTRAT analysis.
  • Duplicates and first degree relatives.
  • Incompatible recorded gender.

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p31.3chr1:61287283-61384764NFIA  rs6691768A > G0.3781.19e-07C1.11 (1.06-1.15)C
1p36.11chr1:24901186-24981785RUNX3  rs10903122G > A0.4801.73e-10C1.12 (1.09-1.18)C
1p36.23chr1:7858046-8146070TNFRSF9  PARK7  rs12727642C > A0.1859.11e-08C1.14 (1.09-1.20)C
1p36.32chr1:2431888-2879054TNFRSF14  MMEL1  rs3748816A > G0.3393.28e-09C1.12 (1.09-1.18)C
1q24.2chr1:167197279-167474186CD247  rs864537A > G0.3913.80e-07C1.1 (1.06-1.15)C
1q24.3chr1:172681545-172912687FASLG  TNFSF4  TNFSF18  rs859637G > A0.4861.75e-06C1.10 (1.06-1.14)C
1q31.2chr1:192500477-192579099RGS1  rs2816316A > C0.1602.20e-17C1.25 (1.19-1.32)C
1q32.1chr1:200893429-201069559rs296547G > A0.3574.11e-09C1.12 (1.09-1.16)C
2p14chr2:68309121-68455124PLEK  rs17035378A > G0.2787.79e-09C1.14 (1.09-1.19)C
2p16.1chr2:60701232-61642429AHSA2  REL  rs13003464A > G0.4013.71e-13C1.15 (1.11-1.20)C
2q12.1chr2:102238781-102651983IL18R1  IL18RAP  IL1RL1  IL1RL2  rs917997G > A0.2361.11e-15C1.19 (1.14-1.25)C
2q31.3chr2:180933651-181404099ITGA4  UBE2E3  rs13010713A > G0.4484.74e-11C1.13 (1.09-1.18)C
2q33.2chr2:203813694-203952558CTLA4  CD28  ICOS  rs4675374G > A0.2235.79e-09C1.14 (1.09-1.19)C
3p21.31chr3:45866656-46467034CCR9  CCRL2  CCR2  CCR5  CCR3  CCR1  rs13098911G > A0.0973.26e-17C1.30 (1.23-1.39)C
3p22.3chr3:32872212-33057492CCR4  rs13314993A > C0.4643.27e-09C1.13 (1.08-1.17)C
3q13.33chr3:119383611-119581808POGLUT1  CD80  rs11712165A > C0.3948.03e-09C1.13 (1.08-1.17)C
3q25.33chr3:159857988-160002484IL12A  rs17810546A > G0.1253.98e-28C1.36 (1.29-1.44)C
3q26.2chr3:169635396-169886565rs10936599G > A0.2524.57e-07C1.12 (1.07-1.16)C
3q28chr3:188351572-188422865LPP  rs1464510C > A0.4852.98e-40C1.29 (1.25-1.34)C
4q27chr4:122017479-122644147IL21  IL2  rs13151961A > G0.1422.18e-27C1.35 (1.28-1.43)C
6p25.3chr6:375936-427152IRF4  rs1033180G > A0.0805.58e-08C1.21 (1.13-1.29)C
6q15chr6:90097116-90316707MAP3K7  BACH2  rs10806425C > A0.3973.89e-10C1.13 (1.09-1.17)C
6q22.33chr6:127633469-128020756PTPRK  THEMIS  rs802734A > G0.3112.62e-14C1.17 (1.12-1.22)C
6q23.3chr6:137552553-137804198TNFAIP3  rs2327832A > G0.2164.46e-19C1.23 (1.17-1.28)C
6q25.3chr6:158897742-159119181TAGAP  rs1738074G > A0.4342.94e-15C1.16 (1.12-1.21)C
7p14.1chr7:37318708-37399609ELMO1  rs6974491G > A0.1701.56e-07C1.14 (1.09-1.20)C
8q24.21chr8:128130288-128286991rs9792269A > G0.2383.28e-09C1.14 (1.1-1.19)C
10q22.3chr10:79256182-79313071ZMIZ1  rs1250552A > G0.4669.09e-10C1.12 (1.09-1.16)C
11q24.3chr11:128468236-128555266ETS1  rs11221332G > A0.2375.28e-16C1.21 (1.16-1.27)C
12q24.12chr12:111284392-112592683SH2B3  rs653178A > G0.4957.15e-21C1.20 (1.15-1.24)C
13q14.2chr13:50160568-50490165rs2762051G > A0.1846.64e-07C1.13 (1.08-1.18)C
14q24.1chr14:68698241-68851345ZFP36L1  rs4899260G > A0.2633.92e-07C1.12 (1.07-1.16)C
16p13.13chr16:11213167-11383900CIITA  SOCS1  CLEC16A  rs12928822G > A0.1613.12e-08C1.16 (1.1-1.22)C
17q21.31chr17:45998697-46810843rs2074404A > C0.2501.23e-06C1.11 (1.06-1.16)C
18p11.21chr18:12738414-12925254PTPN2  rs1893217A > G0.1652.52e-10C1.17 (1.12-1.23)C
21q22.3chr21:44177696-44284761CH507-9B2.1  ICOSLG  rs4819388G > A0.2802.46e-09C1.14 (1.09-1.19)C
22q11.21chr22:21454896-21649639UBE2L3  YDJC  rs2298428G > A0.2011.84e-07C1.13 (1.08-1.19)C
MHCchr6:32414162-32714887HLA-DQA1  HLA-DQB1  HLA-DQA2  rs2187668G > A0.2581.00e-50C6.23 (5.95-6.52)C
Xp22.2chrX:12892402-13005960TLR7  TLR8  rs5979785A > G0.2636.36e-08C1.14 (1.09-1.19)C

Criteria

GDXHsS00038 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date