Genes inproximity | Chr | SNP | SNPgroup | A1 | A2 | P_CD_GWAS | CMH_R1 | CMH_R1+GWAS | OR_R1+GWAS | P valueR2 | ORR2 | CMHGWAS+R1+R2 | ORGWAS+R1+R2 | P_WTCCCCrohn* | P_WTCCCT1D* | P_WTCCCRA* | CMH_AID** |
REL | 2 | rs842647 | 2 | G | A | 0.0274 | 0.00010 | 9.26E-06 | 0.85 | 0.016 | 0.79 | 5.20E-07 | 0.84 | 0.8478 | 0.1157 | 0.7909 | 0.002 |
REL/PEX13 | 2 | rs1729657 | 1 | A | G | 0.0029 | 0.00657 | 1.00E-04 | 0.87 | 0.204 | 0.89 | 4.75E-05 | 0.87 | 0.7933 | 0.9226 | 0.8118 | 0.001 |
AFF3-LONRF2 | 2 | rs1160542 | 3 | G | A | 0.0059 | 0.00360 | 6.68E-05 | 1.15 | 0.048 | 0.84 | 3.97E-03 | 1.10 | 0.8781 | 0.0007 | 0.0037 | 2.49E-06 |
CD80 | 3 | rs1599796 | 2 | A | G | 0.0041 | 0.00241 | 4.07E-05 | 1.20 | 0.281 | 1.12 | 3.16E-05 | 1.18 | 0.1056 | 0.1505 | 0.9814 | 0.112 |
OLIG3-TNFAIP3 | 6 | rs2327832 | 3 | G | A | 0.0029 | 0.00063 | 6.61E-06 | 1.21 | 7.9E-05 | 1.53 | 1.31E-08 | 1.25 | 0.2438 | 0.0046 | 0.0001 | 3.78E-12 |
TCC22D1 | 13 | rs9533935 | 3 | C | A | 0.0048 | 0.00594 | 9.13E-05 | 1.15 | 0.835 | 1.02 | 2.04E-04 | 1.13 | 0.6872 | 0.0151 | 0.9735 | 0.121 |
SNP group indicates the group of SNPs selected (as indicated in the text and supplementary information online).
R1 (replication cohort 1) included 1648 cases and 3258 controls from three populations.
R2 (replication cohort 2) included 538 cases and 593 controls from Italy.
The cohort used in our genome-wide association study (GWAS) in coeliac disease had 767 cases and 1422 controls (see supplementary information online).
*p Values calculated for the WTCCC cases versus NBS (normal blood sample) controls.
**p Values calculated using Cochran–Mantel–Haenszel in which all four coeliac disease populations were summed and considered as one cohort; and Crohn’s disease, RA and T1D cohorts from WTCCC (imputed genotypes) were compared to NBS-WTCCC controls.
AID, autoimmune diseases, here includes coeliac disease (all samples included in the current project), and WTCCC cohorts of Crohn’s disease, type 1 diabetes (T1D) and rheumatoid arthritis (RA); Chr, chromosome; CMH, Cochran–Mantel–Haenszel meta-analysis; OR, odds ratio; WTCCC, Wellcome Trust Case Control Consortium.