CD-RA meta-analysis GWAS and replication—opposite allelic effect method.

Opposite allelic effect meta-analysis of CD and RA. CD-RA GWAS meta-analysis, GWAS results for CD and RA, replication and combined meta-analysis results for loci that achieve P<1×10-5 in CD-RA meta-analysis and P<0.01 in GWAS in CD and RA risk (one SNP per loci). Listed are the rs ID for each SNP, the chromosomal location, one candidate gene in the region (selected by GRAIL analysis, expression analysis or manually based on immunological function; see text and Tables S8, S9, S10 and Table 4), minor alleles (column MinAll) (positive strand in HapMap release 22, major/minor based on frequency in CD GWAS controls). The association P-value and odds ratio (OR) with respect to minor allele are listed for CD and RA GWAS, CD-RA-meta analysis on GWAS, replication analyses in each disease and meta-analysis of CD-RA GWAS and replication cohorts. A – replication in current study with all available CD samples, as described in Materials and Methods; B - replication in current study with all available RA samples; C – replication in current study with RA replication cohort R1, R2 and R3 (failed in R4 and R5); D – replication in current study with RA replication cohorts R1, R2, R3 and R4 (failed in R5), see Table S11 for cohort description; E - The TGFBR3 SNP fit the replication criteria but was not included to the replication step for technical reasons. F - The CD-RA P META MAX column shows the P-overall for SNP included to the replication in both CD and RA. Rs19126261 in TGFBR3 locus was not included to the replication step; in this case the CD-RA P META MAX column shows the p-value for GWAS meta-analysis. P-values are 2-tailed except for replication p-values in CD and RA, indicated by *.