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 PPTables 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 *.