Results from the meta-analysis, replication, and combined analysis.

The meta-analysis was performed using a directional non-weighed Z-score method as explained in the methods section. Combined analyses were performed using a directional weighed Z-score method within diseases and a directional non-weighed Z-score method between diseases. Results for the combined analysis are given only for the SNPs that pass the replication thresholds (directionality in each disease and p-value <0.0071 for the combined replication data).
*, IL18RAP and PTPN2 were not followed up because they are known shared risk loci for CD and CelD;
**, OR for the replication is reported for the allele identified as the risk allele in the initial scan;
#, SNPs that were imputed in the CelD replication datasets.
N.T., not tested. CelD  =  Celiac disease, CD  =  Crohn's disease, SNP  =  single nucleotide polymorphism, IL18RAP  =  interleukin 18 receptor accessory protein, PTPN2  =  protein tyrosine phosphatase, PUS10  =  pseudouridylate synthase 10, CCDC91  =  coiled-coil domain containing 91, TAGAP  =  T-cell activation RhoGTPase activating protein, KCNG4  =  potassium voltage-gated channel, subfamily G, member 4, non-receptor type 2, C10orf72  =  Chromosome 10 open reading frame 72, FERMT1  = - fermitin family homolog 1, 3q13, 9q13, 17p13  =  intergenic regions.