Table 2 Association of single nucleotide polymorphisms (SNPs) with p<1×10−4 in the replication cohorts, WTCCC data, and in the combined analysis
Genes inproximityChrSNPSNPgroupA1A2P_CD_GWASCMH_R1CMH_R1+GWASOR_R1+GWASP valueR2ORR2CMHGWAS+R1+R2ORGWAS+R1+R2P_WTCCCCrohn*P_WTCCCT1D*P_WTCCCRA*CMH_AID**
REL2rs8426472GA0.02740.000109.26E-060.850.0160.795.20E-070.840.84780.11570.79090.002
REL/PEX132rs17296571AG0.00290.006571.00E-040.870.2040.894.75E-050.870.79330.92260.81180.001
AFF3-LONRF22rs11605423GA0.00590.003606.68E-051.150.0480.843.97E-031.100.87810.00070.00372.49E-06
CD803rs15997962AG0.00410.002414.07E-051.200.2811.123.16E-051.180.10560.15050.98140.112
OLIG3-TNFAIP36rs23278323GA0.00290.000636.61E-061.217.9E-051.531.31E-081.250.24380.00460.00013.78E-12
TCC22D113rs95339353CA0.00480.005949.13E-051.150.8351.022.04E-041.130.68720.01510.97350.121

  • 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.