Overview

An association study using 12,041 individuals with celiac disease and 12,228 controls genotyped using ImmunoChip platform. Of those variants assayed 139,553 were found to be polymorphic (at least 2 defined genotype groups). After extensive QC, logistic regression analysis was carried out using PLINK v1.07 and 13 new celiac disease risk loci were identified bringing total number of risk loci to 40. 29 of the 54 fine-mapped signals localised to single genes or gene regulatory elements.

Study Type
Case-Control Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryCEL1204112228--
Exclusion Criteria

Samples were excluded due to :-

  • Low call rate(<99.5%).
  • Incompatible recorded and genotype-inferred gender.
  • Duplication.
  • Evidence for a first or second-degree relative within the dataset.

Markers were excluded due to :-

  • Low call rate (<99.5%).
  • Deviation from Hardy-Weinberg equilibrium in controls (P< 0.0001) 
  • Differential missingness in no-call genotypes between cases and controls (P<0.001).
  • Non-polymorphism, where only one of three expected genotype clouds were observed.

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p36.11chr1:24897830-24981785RUNX3  rs72657048G > C0.4983.80e-06D1.09D
1p36.32chr1:2431888-2879054MMEL1  TTC34  FAM213B  rs4445406T > C0.3445.40e-12D1.15D
1q24.3chr1:172718730-172972573rs12142280T > A0.1808.30e-09D1.15D
1q24.3chr1:172681545-172896352FASLG  rs12068671T > C0.1851.40e-10D1.16D
1q31.2chr1:192500477-192579099RGS1  rs1359062G > C0.1802.50e-25D1.3D
1q31.2chr1:192500477-192578911rs72734930G > A0.0223.70e-04D1.23D
1q32.1chr1:200893429-201069559C1orf106  rs10800746C > T0.3052.60e-08D1.12D
2p13.3chr2:68309121-68612631rs10167650T > G0.2661.30e-04D1.09D
2p16.1chr2:60701232-61642429PUS10  rs13003464A > G0.3884.30e-16D1.17D
2q12.1chr2:102238838-102651983IL18RAP  rs990171C > A0.2251.20e-16D1.20D
2q31.3chr2:180933651-181404099rs1018326T > C0.4183.10e-16D1.16D
2q32.3chr2:191032814-191166501STAT4  rs6752770A > G0.2961.30e-06D1.10D
2q32.3chr2:190990795-191143008STAT4  rs12998748G > T0.1192.60e-04D1.11D
2q32.3chr2:190963960-191109606STAT4  rs6715106A > G0.0588.40e-09D1.27D
2q33.2chr2:203775181-203952558rs34037980A > G0.2171.60e-05D1.1D
2q33.2chr2:202815568-203817550rs10207814C > T0.0391.30e-04D1.20D
2q33.2chr2:203581104-203854006rs1980422T > C0.2331.40e-15D1.19D
3p21.31chr3:45866656-46467034rs7616215T > C0.3618.60e-09D1.12D
3p21.31chr3:46061249-46593299LTF  rs60215663None > None0.0704.80e-05D1.16D
3p21.31chr3:45993605-46585099rs2097282T > C0.3141.10e-20D1.20D
3p22.3chr3:32971574-33130167rs4678523T > C0.3132.40e-07D1.11D
3q13.33chr3:119383611-119581808ARHGAP31  rs61579022G > A0.3909.90e-09D1.11D
3q25.33chr3:159859541-160002484rs2561288C > T0.4558.10e-08D1.12D
3q25.33chr3:159855940-160002484rs76830965C > A0.1112.60e-27D1.36D
3q25.33chr3:159760209-159983443rs1353248C > T0.2889.80e-09D1.14D
3q28chr3:188351572-188422865LPP  rs2030519G > A0.4863.00e-49D1.32D
4q27chr4:122016043-122644147ADAD1  IL21  IL2  KIAA1109  rs62323881C > A0.0738.60e-05D1.15D
4q27chr4:122061159-122691355ADAD1  IL21  IL2  KIAA1109  rs13132308A > G0.1661.90e-38D1.41D
6p25.3chr6:379528-466368IRF4  rs12203592C > T0.1832.60e-04D1.1D
6p25.3chr6:380341-467414IRF4  rs1050976C > T0.4881.80e-09D1.12D
6q15chr6:90097116-90309585BACH2  rs7753008T > C0.3802.70e-07D1.10D
6q22.33chr6:127634953-128020756PTPRK  rs72975916C > T0.1501.20e-05D1.12D
6q22.33chr6:127634953-128020756PTPRK  rs55743914C > T0.2391.10e-18D1.21D
6q23.3chr6:137567471-137805141rs77027760G > A0.1902.10e-07D1.14D
6q23.3chr6:137568133-137806067rs17264332A > G0.2115.00e-30D1.29D
6q25.3chr6:158905798-159123547rs1107943T > C0.0712.80e-06D1.18D
6q25.3chr6:158897742-159120449TAGAP  rs182429A > G0.4278.50e-16D1.16D
7p14.1chr7:37323977-37400850ELMO1  rs79758729A > G0.1012.10e-08D1.18D
8q24.21chr8:128129610-128286991rs10808568A > C0.2562.20e-05D1.1D
10p15.1chr10:6346109-6394072rs2387397C > G0.2291.90e-08D1.14D
10q22.3chr10:79256182-79313071ZMIZ1  rs1250552A > G0.4708.00e-17D1.16D
11q23.1chr11:111306494-111439834POU2AF1  COLCA2  rs7104791C > T0.2091.90e-11D1.16D
11q23.3chr11:118444134-118902495rs10892258G > A0.2371.70e-11D1.16D
11q24.3chr11:128471593-128555989ETS1  rs61907765C > T0.2133.40e-13D1.18D
12q24.12chr12:111278572-112592683SH2B3  ATXN2  rs3184504C > T0.4885.40e-21D1.19D
14q24.1chr14:68696393-68851345ZFP36L1  rs11851414T > C0.2214.70e-08D1.13D
15q24.1chr15:74319440-75160834CLK3  CSK  rs1378938C > T0.2787.80e-09D1.13D
16p13.13chr16:11210761-11381471rs80073729G > A0.0041.30e-04D1.70D
16p13.13chr16:11193176-11372654SOCS1  rs243323A > G0.3002.50e-05D1.09D
16p13.13chr16:11212430-11382294rs9673543A > G0.1692.00e-04D1.10D
16p13.13chr16:10830201-10902542CIITA  rs6498114T > G0.2465.80e-10D1.14D
18p11.21chr18:12738414-12926279PTPN2  rs62097857G > A0.0405.20e-05D1.20D
18p11.21chr18:12738414-12926279PTPN2  rs11875687T > C0.1501.90e-10D1.17D
21q22.3chr21:44170097-44277872rs58911644A > T0.1936.20e-07D1.12D
21q22.3chr21:42389975-42471211UBASH3A  rs1893592A > C0.2823.00e-09D1.14D
22q11.21chr22:21454896-21649639YDJC  UBE2L3  rs4821124T > C0.1865.70e-11D1.16D
Xq28chrX:153853745-154120938IRAK1  HCFC1  rs13397None > None0.1332.70e-08D1.18D

Criteria

GDXHsS00009 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date