CD-RA meta-analysis and replication, directional analysis.

Directional 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−5 in CD-RA meta-analysis and PTables 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 GWAS meta-analysis, replication analyses in each disease and meta-analysis of CD-RA GWAS and replication cohorts. Loci established in both diseases are not included in this table. A – replication for this SNP in CD was done in Dubois et al paper [2]; B – replication in current study with all available CD samples as described in Materials and Methods; C - replication for this SNP in RA was done in Stahl et al paper [3]; D - replication in current study with all available RA samples, as described in methods; E – replication in current study with RA replication cohort R1, R2, R3 and R5 (failed in R4); F – replication in current study with RA replication cohorts R1, R2, R3 and R4 (failed in R5) (see Table S11 for cohort description); G – ICOSLG (established CD locus) and PRKCQ (established RA locus) SNPs were not included to the replication and not mentioned in this table. H - The CD-RA P META MAX column shows the P-overall for SNP tested in replication in both CD and RA. For one SNP (ANKRD55) the replication results were available only in CD replication cohort, in this case the CD-RA P META MAX column shows the p-value for the meta-analysis of CD-RA GWAS and CD-replication. P-values are 2-tailed except for replication p-values in CD and RA, indicated by *.