Overview

A GWA scan of 5,956 cases and 14,927 controls for Crohn's disease (CD) was carried out using HapMap phase 3 (CEU+TSI) data to impute 1.23M SNPs. Imputation was carried out using Beagle 3.1 and association was calculated using PLINK. A meta-analysis was perfomed by combining the above, filtered by P.association < 0.01, with a replication cohort of 14,763 Crohn's disease cases and 15,977 controls genotyped on the ImmunoChip platform. This identified 30 (16 novel) loci specific to Crohn's disease with a further 76 (24 novel) being indistinguishable from the related IBD disorder, ulcerative colitis. A further 64 loci reached genomewide significance in a combined analysis of Crohn's disease and ulcerative colitis (IBD), these are shown on the IBD study page

Study Type
Whole Genome Association Study
Samples
GroupPhenotypePopulationCasesControlsFamiliesTrios
DiscoveryCRO59378043--
ReplicationCRO1476315977--
Exclusion Criteria

Discovery

In addition to previously reported cohort QC, samples were excluded due to...

  • Call rate <98%
  • Heterozygosity ±0.2

Markers were excluded due to...

  • HWE (controls) P<10-6
  • HWE (cases) P<10-10
  • Call rate <95%
  • Difference in call rate between cases and controls > 2%

Replication

Samples

  • Call rate <95%
  • Heterozygosity outside CI 95% per batch
  • Non-European ancestry
  • Abnormal mean-intensity values
  • Duplicate and closely-related samples

Markers

  • Call rate <98%
  • HWE P<10-10
  • Manual QC for those SNPs with meta-analysis P<10-5

Study Association

RegionLocationGene(s)MarkerAlleleMAFP ValueOdds Ratio
1p12chr1:119807450-120084479ADAM30  rs3897478T > C0.1101.97e-11C1.16 (1.1-1.22)C
1p13.2chr1:113288123-114002809DCLRE1B  PTPN22  rs6679677C > A0.0982.03e-15C1.19 (1.12-1.27)C
1p31.1chr1:70524556-70651887rs2651244G > A0.3972.14e-04C1.03 (0.99-1.06)C
1p31.1chr1:77522888-78355813rs17391694C > T0.1262.96e-09C1.14 (1.08-1.19)C
1p31.3chr1:67128876-67302310IL23R  IL12RB2  rs11209026G > A0.0671.02e-146C2.38 (2.17-2.56)C
1p36.12chr1:22326008-22411939rs12568930T > C0.1691.32e-03C1.06 (1.01-1.11)C
1p36.23chr1:7853370-8140630TNFRSF9  rs35675666G > T0.1691.13e-07C1.1 (1.05-1.15)C
1p36.33chr1:1190173-1452909TNFRSF18  TNFRSF4  rs12103G > A0.1816.96e-08C1.09 (1.04-1.13)C
1q21.3chr1:151565936-152018664RORC  rs4845604G > A0.1471.88e-06C1.11 (1.05-1.16)C
1q22chr1:155052885-156118465RIT1  UBQLN4  MSTO1  rs670523G > A0.3245.79e-11C1.09 (1.05-1.12)C
1q23.3chr1:160727284-160979324CD48  CD244  ARHGAP30  USF1  ITLN1  F11R  SLAMF7  SLAMF1  rs4656958G > A0.3171.12e-05C1.05 (1.02-1.09)C
1q23.3chr1:161419627-161668253HSPA6  FCRLA  FCGR3A  FCGR3B  FCGR2B  FCGR2A  rs1801274A > G0.4751.53e-07C1.08 (1.04-1.11)C
1q24.3chr1:172711325-172972573FASLG  TNFSF18  rs9286879A > G0.2365.53e-22C1.13 (1.08-1.17)C
1q31.3chr1:197342098-197969200C1orf53  rs2488389G > A0.2128.45e-13C1.12 (1.08-1.17)C
1q32.1chr1:200892467-201069559KIF21B  rs7554511C > A0.2807.81e-19C1.15 (1.11-1.19)C
1q32.1chr1:206709013-206867232FCMR  IL19  MAPKAPK2  IL10  PIGR  IL20  IL24  RASSF5  rs3024505G > A0.1592.48e-19C1.16 (1.11-1.21)C
2p14chr2:65250869-65490608SPRED2  rs6740462A > C0.2601.06e-08C1.11 (1.06-1.15)C
2p15chr2:62256286-62420888rs10865331G > A0.3749.77e-10C1.10 (1.06-1.13)C
2p16.1chr2:60706158-61642429KIAA1841  AHSA2  C2orf74  REL  rs7608910A > G0.3926.92e-19C1.13 (1.09-1.17)C
2p21chr2:43221519-43708586rs10495903C > T0.1348.03e-12C1.11 (1.06-1.17)C
2p23.2chr2:28377859-28449611FOSL2  BRE  rs925255C > T0.4562.67e-15C1.12 (1.09-1.16)C
2p23.3chr2:24464482-25234839ADCY3  rs6545800C > T0.4346.14e-16C1.14 (1.10-1.18)C
2p23.3chr2:27154127-28142797UCN  rs1728918G > A0.4094.86e-16C1.12 (1.09-1.16)C
2q12.1chr2:102238781-102651983IL18RAP  IL1RL1  IL1R2  IL18R1  IL1R1  IL1RL2  rs917997C > T0.2353.12e-20C1.14 (1.10-1.18)C
2q24.2chr2:162104363-162502867IFIH1  rs2111485G > A0.3911.02e-03C1.05 (1.02-1.09)C
2q32.3chr2:190986040-191143008STAT4  STAT1  rs1517352C > A0.3921.93e-10C1.1 (1.05-1.14)C
2q35chr2:218074907-218395928TMBIM1  CTDSP1  CXCR2  ARPC2  SLC11A1  PNKD  CXCR1  rs2382817C > A0.3991.28e-07C1.09 (1.05-1.12)C
2q37.1chr2:233232538-233674416INPP5D  ATG16L1  rs12994997A > G0.4694.14e-70C1.23 (1.19-1.27)C
2q37.1chr2:230181042-230371171SP140  rs6716753T > C0.1911.17e-16C1.13 (1.09-1.18)C
2q37.3chr2:240619922-240712978GPR35  rs3749171C > T0.1773.02e-08C1.11 (1.06-1.15)C
3p21.31chr3:48465783-50711580PFKFB4  IP6K1  USP4  UCN2  GPX1  MST1  MST1R  IP6K2  BSN  rs3197999G > A0.2795.31e-29C1.16 (1.12-1.20)C
3p24.3chr3:18566300-18808423rs4256159C > T0.1459.00e-15C1.15 (1.10-1.21)C
4p11chr4:48158462-52069158TXK  SLC10A4  rs6837335G > A0.3521.75e-08C1.09 (1.05-1.12)C
4q13.3chr4:73859603-74142734CXCL1  CXCL5  PF4V1  PF4  CXCL6  CXCL8  CXCL3  CXCL2  rs2472649G > A0.1132.13e-02C1.08 (1.02-1.14)C
4q24chr4:101782996-102192580rs13126505G > A0.0672.33e-10C1.17 (1.10-1.25)C
4q27chr4:122017479-122644147IL21  IL2  rs7657746A > G0.2461.01e-09C1.11 (1.06-1.15)C
5p13.1chr5:40286865-40626651PTGER4  rs11742570C > T0.3901.81e-82C1.3 (1.25-1.33)C
5p15.2chr5:10667329-10833902DAP  rs2930047T > C0.3741.45e-07C1.08 (1.04-1.12)C
5q11.2chr5:56121772-56154384IL6ST  IL31RA  rs10065637C > T0.2123.68e-12C1.12 (1.08-1.16)C
5q13.2chr5:73161293-73284584rs7702331A > G0.3255.63e-10C1.09 (1.05-1.12)C
5q15chr5:96743698-97141497LNPEP  ERAP1  ERAP2  rs1363907G > A0.4285.62e-13C1.07 (1.04-1.11)C
5q23.3chr5:130189256-131985036rs4836519T > C0.3034.24e-10C1.09 (1.05-1.14)C
5q31.1chr5:132075186-132658977IL3  PDLIM4  IRF1  IL5  IL4  SLC22A5  CSF2  IL13  ACSL6  SLC22A4  rs2188962C > T0.4201.35e-52C1.22 (1.18-1.26)C
5q31.3chr5:142033064-142260854SPRY4  NDFIP1  rs6863411T > A0.3763.59e-14C1.1 (1.06-1.14)C
5q33.1chr5:150658703-151012930TNIP1  IRGM  rs11741861A > G0.0752.94e-37C1.32 (1.25-1.40)C
5q33.3chr5:159397971-159460964IL12B  rs6871626C > A0.3334.04e-36C1.20 (1.16-1.24)C
5q35.2chr5:173797287-174112331CPEB4  rs17695092T > G0.2934.68e-09C1.1 (1.05-1.14)C
5q35.3chr5:177079730-177421018DOK3  rs12654812G > A0.3431.90e-04C1.06 (1.03-1.10)C
6p22.3chr6:20639373-21029922rs9358372A > G0.3758.66e-14C1.11 (1.07-1.14)C
6p22.3chr6:21338901-21476386rs12663356C > T0.4684.01e-12C1.1 (1.06-1.14)C
6p23chr6:14691381-14736360rs17119A > G0.1948.51e-09C1.08 (1.04-1.12)C
6q15chr6:90097116-90319078rs1847472C > A0.3461.57e-10C1.09 (1.05-1.12)C
6q21chr6:111075054-111647042TRAF3IP2  FYN  REV3L  rs3851228A > T0.0644.02e-07C1.14 (1.07-1.21)C
6q21chr6:105954686-106099497rs6568421A > G0.2888.24e-20C1.14 (1.10-1.18)C
6q22.33chr6:126764254-127221808rs9491697A > G0.4583.79e-10C1.08 (1.04-1.11)C
6q22.33chr6:127629641-128019645rs13204742G > T0.1278.38e-15C1.17 (1.12-1.23)C
6q23.3chr6:137568592-137806067TNFAIP3  rs6920220G > A0.2092.22e-03C1.06 (1.02-1.10)C
6q24.2chr6:143504346-143711180PHACTR2  rs12199775A > G0.0705.43e-07C1.15 (1.08-1.23)C
6q25.3chr6:158903940-159121739TAGAP  rs212388T > C0.3963.04e-14C1.11 (1.07-1.14)C
6q27chr6:166931410-167134466RNASET2  RP11-517H2.6  RPS6KA2  CCR6  rs1819333T > G0.4636.76e-21C1.11 (1.08-1.15)C
7p12.2chr7:50206640-50325467IKZF1  ZPBP  rs1456896T > C0.3167.28e-15C1.11 (1.06-1.15)C
7p15.1chr7:28080094-28222707CREB5  JAZF1  rs864745C > T0.4973.65e-09C1.09 (1.05-1.12)C
7p15.2chr7:26618343-27162670rs10486483G > A0.2392.56e-08C1.09 (1.05-1.13)C
7q22.1chr7:99119190-99271073SMURF1  rs9297145A > C0.2561.64e-08C1.09 (1.05-1.13)C
7q22.1chr7:100502511-100911543EPO  rs1734907G > A0.1611.67e-13C1.16 (1.11-1.21)C
7q31.2chr7:117234417-117597881rs38904T > C0.4713.76e-03C1.04 (1.0-1.08)C
8q21.3chr8:89628493-89942373RIPK2  rs7015630T > C0.2631.42e-08C1.08 (1.03-1.11)C
8q24.13chr8:125438839-125562774TRIB1  rs921720G > A0.3738.30e-20C1.11 (1.08-1.15)C
8q24.21chr8:129468135-129685804rs1991866C > G0.4328.95e-07C1.07 (1.03-1.10)C
8q24.21chr8:128484980-128585383rs6651252T > C0.1281.45e-16C1.19 (1.12-1.25)C
9p24.1chr9:4944089-5274545JAK2  rs10758669A > C0.3471.44e-31C1.18 (1.14-1.22)C
9q22.31chr9:91134438-91402091NFIL3  rs4743820T > C0.2964.90e-04C1.03 (1.0-1.08)C
9q32chr9:114715997-114937465TNFSF8  TNC  TNFSF15  rs4246905C > T0.2896.23e-26C1.15 (1.1-1.19)C
9q34.3chr9:136243135-136514725CARD9  INPP5E  SDCCAG3  PMPCA  rs10781499G > A0.4233.49e-48C1.21 (1.17-1.25)C
10p11.21chr10:34887225-35588558CREM  rs11010067C > G0.3522.49e-25C1.16 (1.12-1.20)C
10p11.23chr10:30398004-30522007MAP3K8  rs1042058C > T0.3985.93e-11C1.09 (1.05-1.12)C
10p15.1chr10:5987834-6098857IL2RA  IL15RA  rs12722515C > A0.1603.76e-10C1.12 (1.08-1.18)C
10q21.1chr10:58064134-58408714CISD1  IPMK  rs2790216G > A0.2168.07e-09C1.08 (1.03-1.12)C
10q21.2chr10:62581266-62866159rs10761659G > A0.4596.37e-46C1.2 (1.16-1.25)C
10q22.2chr10:73639542-73945471rs2227564C > T0.2706.75e-10C1.1 (1.06-1.15)C
10q22.3chr10:79237086-79312766rs1250546A > G0.4233.15e-18C1.12 (1.09-1.16)C
10q23.1chr10:80326790-80603584TSPAN14  FAM213A  rs6586030G > A0.2049.24e-16C1.15 (1.1-1.19)C
10q23.33chr10:92439580-92742146rs7911264C > T0.4304.84e-05C1.06 (1.02-1.09)C
10q24.2chr10:99508770-99570210NKX2-3  rs4409764G > T0.4821.80e-41C1.18 (1.14-1.22)C
11p15.5chr11:1845142-1946041LSP1  TNNI2  rs907611G > A0.3186.77e-05C1.06 (1.02-1.10)C
11q12.1chr11:58132360-58690335CNTF  LPXN  rs10896794T > C0.2491.21e-05C1.09 (1.04-1.12)C
11q12.2chr11:60962649-61068645PTGDR2  CD6  CD5  rs11230563C > T0.3471.89e-10C1.09 (1.05-1.14)C
11q12.2chr11:61749438-61917078FADS1  MYRF  FADS2  rs4246215G > T0.3281.93e-15C1.11 (1.08-1.15)C
11q13.1chr11:64081858-64457156TRPT1  RPS6KA4  FLRT1  CCDC88B  rs559928C > T0.1884.22e-09C1.09 (1.04-1.14)C
11q13.1chr11:65604133-66296655CTSW  RELA  FOSL1  SNX32  rs2231884C > T0.1872.91e-10C1.12 (1.07-1.16)C
11q13.5chr11:76324636-76632292rs2155219T > G0.4989.56e-36C1.19 (1.15-1.23)C
11q14.2chr11:87236723-87522249rs6592362G > A0.2816.98e-05C1.07 (1.03-1.11)C
11q23.3chr11:118606652-118952438CXCR5  rs630923C > A0.2437.07e-09C1.09 (1.05-1.14)C
12p13.2chr12:12384138-12579426BORCS5  rs11612508A > G0.2733.33e-02C1.04 (1.00-1.07)C
12q12chr12:40223113-40613085LRRK2  rs11564258G > A0.0276.38e-29C1.46 (1.32-1.62)C
12q13.11chr12:47788458-47837647VDR  rs11168249T > C0.4619.57e-03C1.03 (1.00-1.07)C
12q15chr12:68036752-68116292IL22  IL26  IFNG  rs7134599G > A0.3894.16e-05C1.05 (1.02-1.09)C
13q12.13chr13:26932960-26990142rs17085007T > C0.1853.79e-03C1.07 (1.02-1.11)C
13q14.11chr13:43662130-44029117LACC1  rs3764147A > G0.2312.19e-21C1.16 (1.11-1.20)C
13q14.11chr13:40435146-40471356rs941823C > T0.2498.45e-04C1.05 (1.01-1.09)C
13q32.3chr13:99110747-99432425GPR18  GPR183  rs9557195T > C0.2201.35e-12C1.12 (1.08-1.16)C
14q24.1chr14:68696738-68851345ZFP36L1  rs194749T > C0.2272.70e-10C1.09 (1.05-1.13)C
14q24.3chr14:75204956-75283172FOS  MLH3  rs4899554C > T0.1722.71e-08C1.1 (1.05-1.15)C
14q31.3chr14:87863352-88175959GALC  GPR65  rs8005161C > T0.0861.96e-12C1.16 (1.09-1.22)C
15q14chr15:38522176-38679976RASGRP1  SPRED1  rs16967103T > C0.1943.88e-09C1.09 (1.05-1.13)C
15q22.33chr15:67120258-67176997SMAD3  rs17293632C > T0.2405.97e-16C1.10 (1.06-1.14)C
15q26.1chr15:90382489-90725453CRTC3  rs7495132C > T0.1036.61e-08C1.14 (1.08-1.2)C
16p11.2chr16:28283985-29014657IL27  SULT1A1  EIF3C  NUPR1  RABEP2  SULT1A2  rs26528T > C0.4599.65e-22C1.13 (1.10-1.17)C
16p12.2chr16:23720685-23964030PRKCB  rs7404095C > T0.4241.61e-05C1.05 (1.02-1.09)C
16p13.13chr16:11210761-11380893RMI2  SOCS1  LITAF  rs529866C > T0.2021.73e-16C1.18 (1.12-1.22)C
16q12.1chr16:50658453-50824433ADCY7  NOD2  rs2066847- > T0.1785.61e-166C1.56 (1.50-1.62)C
16q24.1chr16:85949450-85990498IRF8  rs10521318C > T0.0831.92e-08C1.2 (1.14-1.28)C
17q11.2chr17:27286355-27690219LGALS9  LGALS9C  NOS2  rs2945412A > G0.4128.68e-17C1.14 (1.1-1.18)C
17q12chr17:34175049-34352741CCL13  CCL11  CCL2  rs3091316G > A0.2741.22e-26C1.16 (1.12-1.2)C
17q12chr17:39219977-40074859GSDMA  GSDMB  ZPBP2  ORMDL3  IKZF3  rs12946510C > T0.4673.58e-25C1.15 (1.12-1.19)C
17q21.2chr17:42156716-42774617STAT3  STAT5A  STAT5B  rs12942547A > G0.4223.34e-17C1.11 (1.08-1.15)C
17q23.1chr17:59412005-59997425RPS6KB1  TUBD1  rs1292053A > G0.4548.85e-13C1.10 (1.06-1.13)C
18p11.21chr18:12738414-12925254rs1893217A > G0.1603.05e-25C1.18 (1.13-1.24)C
18q21.1chr18:48827214-48922435SMAD7  rs7240004A > G0.3777.50e-04C1.03 (1.0-1.06)C
18q22.2chr18:69831437-69902924CD226  rs727088A > G0.4795.20e-05C1.06 (1.03-1.10)C
19p13.2chr19:10292692-10520699ICAM1  TYK2  PPAN-P2RY11  rs11879191G > A0.2031.78e-17C1.15 (1.1-1.19)C
19p13.3chr19:1090804-1183852GPX4  HMHA1  rs2024092G > A0.2158.26e-22C1.16 (1.11-1.20)C
19q13.11chr19:33219244-33272215CEBPG  rs17694108G > A0.2884.09e-09C1.09 (1.05-1.13)C
19q13.32chr19:46304332-46410492rs4802307G > T0.2922.00e-10C1.1 (1.06-1.14)C
19q13.33chr19:48592641-48763133FUT2  DBP  SPHK2  IZUMO1  rs516246C > T0.4821.00e-15C1.11 (1.07-1.14)C
19q13.42chr19:54783517-54916142NLRP7  NLRP2  KIR2DL1  LILRB4  rs11672983G > A0.3364.00e-04C1.08 (1.04-1.12)C
20q11.21chr20:31995378-32517173HCK  rs6142618G > A0.4432.30e-09C1.09 (1.05-1.12)C
20q11.21chr20:32611779-33001967DNMT3B  rs4911259T > G0.4035.12e-06C1.08 (1.04-1.11)C
20q13.12chr20:45906223-46158839MMP9  PLTP  CD40  rs1569723A > C0.2489.95e-14C1.13 (1.09-1.18)C
20q13.13chr20:50301749-50423945CEBPB  rs913678T > C0.3254.78e-04C1.04 (1.01-1.09)C
20q13.32chr20:59153293-59295301ZNF831  CTSZ  rs259964G > A0.4573.87e-11C1.10 (1.06-1.13)C
20q13.33chr20:63567747-63814828TNFRSF6B  SLC2A4RG  LIME1  ZGPAT  rs6062504G > A0.2982.45e-19C1.12 (1.09-1.16)C
21q21.1chr21:15326120-15470979rs2823286G > A0.2934.63e-28C1.18 (1.14-1.23)C
21q22.2chr21:39081110-39111851rs2836878G > A0.2722.80e-14C1.12 (1.08-1.16)C
21q22.3chr21:44152485-44266077CH507-9B2.1  ICOSLG  rs7282490A > G0.4062.55e-19C1.11 (1.07-1.14)C
21q22.11chr21:33370311-33842379IFNGR2  IFNAR1  IFNAR2  IL10RB  GART  TMEM50B  rs2284553G > A0.3992.14e-16C1.12 (1.09-1.16)C
22q11.21chr22:21454896-21649639CCDC116  UBE2L3  MAPK1  YDJC  RIMBP3  rs2266959G > T0.1903.89e-16C1.13 (1.08-1.17)C
22q12.2chr22:29651931-30271212OSM  MTMR3  LIF  rs2412970A > G0.4525.94e-12C1.08 (1.05-1.12)C
22q13.1chr22:39253129-39364639APOBEC3G  ATF4  TAB1  rs2413583C > T0.1674.35e-31C1.25 (1.19-1.3)C
MHCchr6:31253891-31375183NFKBIL1  PSORS1C1  MICB  HLA-C  rs9264942T > C0.3584.96e-28C1.15 (1.11-1.18)C

Criteria

GDXHsS00021 meets the following criteria:

Criteria Name
Details
Disease Tags
Study for a Disease 

Publications

PMIDTitleFirst AuthorJournalDisease(s)Date