Overview

Meta-analysis of six Crohn’s disease genomewide association studies (GWAS) comprising 6,333 affected individuals (cases) and 15,056 controls of european descent. Genotyping in the six studies was performed on Illumina and Affymetrix platforms. Imputation was done with the BEAGLE software using Hapmap 3 for 5 studies and with the MACH software using Hapmap 2 for 1 study (early-onset). 953,241 SNPs were available for analysis. 51 SNPs were selected for replication in 15,694 cases, 14,026 controls and 414 parent-offspring trios. In total 39 new  Crohn’s disease susceptibility loci were confirmed.

Study Type
Whole Genome Association Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryCRO633315056--
ReplicationCRO1569414026-414
Exclusion Criteria

Any samples with <10% missing data from any experiment were excluded from any further analysis.

Prior to association anlysis, all cluster plots were visually and/or manually checked to check that the SNP had been genotyped well and to confirm that the calling algorithm had correctly called the clusters.

Other criteria applied to the data included call rate >95% in case or control and HW P>10-4 in each control sample.

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p13.2chr1:113296527-114009223PTPN22  rs2476601G > A0.0934.47e-09D1.27 (1.18-1.37)D
1p31.3chr1:67128876-67302310IL23R  rs11209026G > A0.0681.00e-64D2.63 (2.38-3.03)D
1p36.23chr1:7662553-7905951VAMP3  rs2797685G > A0.1907.10e-09C1.05 (1.01-1.10)C
1q22chr1:155047234-156070519SCAMP3  MUC1  rs1142287G > A0.2502.30e-13C1.13 (1.06-1.19)C
1q23.3chr1:160723029-160963275ITLN1  CD244  rs4656940A > G0.1996.17e-07D1.15 (1.09-1.2)D
1q24.3chr1:172710619-172971743FASLG  TNFSF4  TNFSF18  rs7517810C > T0.2461.51e-15D1.22 (1.16-1.28)D
1q31.3chr1:197342098-197969200DENND1B  rs1998598A > G0.3028.70e-09C1.04 (1.00-1.09)C
1q32.1chr1:200892467-201069559C1orf106  KIF21B  rs7554511C > A0.2741.58e-07D1.14 (1.08-1.19)D
1q32.1chr1:206709013-206867232IL19  IL10  rs3024505C > T0.1571.60e-14C1.12 (1.07-1.17)C
2p16.1chr2:60711514-61646880C2orf74  REL  rs10181042C > T0.4206.61e-09D1.14 (1.09-1.19)D
2p21chr2:43221519-43708586THADA  rs10495903C > T0.1291.60e-14C1.14 (1.09-1.20)C
2p23.3chr2:25232520-25398031DNMT3A  rs13428812A > G0.3268.50e-10C1.06 (1.03-1.10)C
2p23.3chr2:27162407-28198514GCKR  rs780093C > T0.4184.70e-11C1.15 (1.10-1.21)C
2q12.1chr2:102238605-102649420IL18R1  IL18RAP  IL1RL1  rs2058660A > G0.2311.58e-12D1.19 (1.14-1.26)D
2q33.1chr2:197277486-198097196PLCL1  rs6738825G > A0.4733.50e-09C1.06 (1.02-1.11)C
2q37.1chr2:230211574-230371171SP140  rs7423615C > T0.1873.10e-13C1.12 (1.07-1.18)C
2q37.1chr2:233232538-233685588ATG16L1  rs3792109T > C0.4716.76e-41D1.33 (1.28-1.41)D
3p21.31chr3:48465783-50711580GPX1  MST1  BSN  rs3197999G > A0.2976.17e-17D1.22 (1.16-1.27)D
3p24.3chr3:18566300-18792674rs13073817G > A0.3226.70e-09C1.08 (1.03-1.13)C
5p13.1chr5:40286865-40626651PTGER4  rs11742570C > T0.3947.08e-36D1.33 (1.27-1.39)D
5q13.2chr5:73161293-73284584rs7702331A > G0.4005.90e-12C1.12 (1.08-1.18)C
5q15chr5:96743698-97141497ERAP2  rs2549794T > C0.4091.10e-10C1.05 (1.02-1.09)C
5q31.1chr5:132101268-132663000SLC22A5  SLC22A4  IRF1  IL3  rs12521868G > T0.4221.41e-20D1.23 (1.18-1.28)D
5q31.3chr5:142033064-142260854NDFIP1  rs11167764C > A0.2042.00e-09C1.06 (1.02-1.11)C
5q33.1chr5:150658703-151012930IRGM  rs7714584A > G0.0887.76e-19D1.37 (1.28-1.47)D
5q33.3chr5:159101624-159399784IL12B  rs6556412G > A0.3325.37e-14D1.18 (1.13-1.24)D
5q35.2chr5:173790939-174111528CPEB4  rs359457T > C0.4292.50e-12C1.08 (1.04-1.12)C
6p22.3chr6:20522059-20919892CDKAL1  rs6908425C > T0.2161.41e-08D1.18 (1.11-1.23)D
6p25.2chr6:3413203-3475869rs17309827T > G0.3616.70e-09C1.1 (1.05-1.16)C
6q15chr6:90097116-90319078BACH2  rs1847472G > T0.3425.10e-09C1.08 (1.03-1.11)C
6q21chr6:105954686-106099497PRDM1  rs6568421A > G0.3014.37e-08D1.13 (1.07-1.18)D
6q25.3chr6:158903940-159121739TAGAP  rs212388A > G0.3932.30e-11C1.10 (1.05-1.14)C
6q27chr6:166931410-167134466RP11-517H2.6  CCR6  rs415890C > G0.4782.51e-12D1.18 (1.12-1.22)D
7p12.2chr7:50206640-50325467IKZF1  ZPBP  FIGNL1  rs1456896T > C0.3101.20e-08D1.14 (1.09-1.2)D
8q24.13chr8:125442131-125562774rs4871611A > G0.3911.51e-12D1.18 (1.12-1.23)D
8q24.21chr8:128484980-128585383rs6651252T > C0.1353.90e-18C1.23 (1.18-1.3)C
9p24.1chr9:4944089-5274545JAK2  rs10758669A > C0.3491.00e-13D1.18 (1.13-1.23)D
9q32chr9:114715997-114937465TNFSF8  TNFSF15  rs3810936C > T0.3181.00e-15D1.2 (1.15-1.27)D
9q34.3chr9:136243135-136514725CARD9  SNAPC4  rs4077515C > T0.4111.30e-36C1.18 (1.13-1.22)C
10p11.21chr10:34896568-35616604CREM  rs12242110A > G0.3151.10e-09D1.15 (1.10-1.20)D
10p15.1chr10:5988280-6131453IL2RA  rs12722489C > T0.1482.90e-09C1.11 (1.05-1.16)C
10q21.1chr10:58064134-58404800UBE2D1  rs1819658C > T0.2269.10e-17C1.19 (1.14-1.25)C
10q21.2chr10:62581266-62866159ZNF365  rs10761659G > A0.4624.37e-22D1.23 (1.18-1.28)D
10q22.3chr10:79258505-79313758ZMIZ1  rs1250550G > T0.3311.10e-30C1.19 (1.15-1.23)C
10q24.2chr10:99508770-99570210NKX2-3  rs4409764G > T0.4922.29e-20D1.22 (1.17-1.27)D
11q12.2chr11:61749438-61917078FADS1  rs102275T > C0.3412.30e-11C1.08 (1.04-1.12)C
11q13.1chr11:64076473-64456055ESRRA  PRDX5  rs694739A > G0.3746.00e-10C1.1 (1.05-1.16)C
11q13.5chr11:76324636-76635258EMSY  rs7927997C > T0.3895.62e-13D1.17 (1.12-1.22)D
12q12chr12:40223113-40613085LRRK2  rs11564258G > A0.0256.17e-21D1.74 (1.55-1.95)D
13q14.11chr13:43662130-44029117LACC1  rs3764147A > G0.2451.41e-10D1.17 (1.12-1.23)D
13q14.11chr13:42247134-42527627TNFSF11  rs2062305A > G0.3464.90e-10C1.10 (1.05-1.15)C
14q24.1chr14:68690375-68851345ZFP36L1  rs4902642G > A0.4161.60e-10C1.08 (1.11-1.04)C
14q31.3chr14:87863352-88175959GALC  GPR65  rs8005161C > T0.1194.20e-18C1.23 (1.16-1.31)C
15q22.33chr15:67120258-67176997SMAD3  rs17293632C > T0.2332.70e-19C1.12 (1.07-1.16)C
16p11.2chr16:28283985-29014657LAT  IL27  CD19  SH2B1  EIF3C  rs151181A > G0.3861.50e-11C1.07 (1.03-1.12)C
16q12.1chr16:50658453-50823782NOD2  rs2076756A > G0.2603.98e-69D1.53 (1.46-1.60)D
17q12chr17:39226421-40083963ZPBP2  ORMDL3  IKZF3  rs2872507G > A0.4581.51e-09D1.14 (1.09-1.19)D
17q12chr17:34175049-34352741CCL2  CCL7  rs3091315A > G0.2771.70e-13D1.2 (1.14-1.27)D
17q21.2chr17:42218659-42872213STAT3  MLX  rs11871801A > C0.2442.51e-08D1.15 (1.1-1.2)D
18p11.21chr18:12738414-12925254PTPN2  rs1893217A > G0.1531.29e-14D1.25 (1.18-1.32)D
19p13.2chr19:10280033-10517872ICAM3  ICAM1  TYK2  rs12720356T > G0.0841.40e-12C1.12 (1.06-1.19)C
19p13.3chr19:1090804-1185547GPX4  SBNO2  rs740495A > G0.2478.13e-12D1.16 (1.10-1.21)D
19q13.11chr19:33235904-33287769rs736289T > C0.3888.70e-09C1.06 (1.02-1.11)C
19q13.33chr19:48593054-48774825FUT2  RASIP1  rs281379G > A0.4877.40e-12C1.07 (1.04-1.11)C
20q13.33chr20:63567747-63814828TNFRSF6B  RTEL1  SLC2A4RG  rs4809330G > A0.2912.70e-15C1.12 (1.06-1.18)C
21q21.1chr21:15326120-15470979rs1736020C > A0.4219.33e-12D1.16 (1.11-1.2)D
21q22.3chr21:44145591-44263692CH507-9B2.1  ICOSLG  rs2838519A > G0.3912.09e-14D1.18 (1.13-1.23)D
22q11.21chr22:21454896-21649639YDJC  rs181359C > T0.2034.80e-16C1.10 (1.06-1.15)C
22q12.2chr22:29710670-30276363MTMR3  rs713875G > C0.4717.30e-12C1.08 (1.04-1.13)C
22q13.1chr22:39253129-39364639TAB1  rs2413583C > T0.1701.10e-26C1.23 (1.18-1.28)C
MHCchr6:31461190-31647390HLA-DQA2  LTB  LST1  LTA  TNF  rs1799964T > C0.2093.98e-11D1.19 (1.13-1.25)D

Criteria

GDXHsS00011 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date