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<1×10−5 in CD-RA meta-analysis and P<0.01 in GWAS in CD and RA risk (one SNP per locus). Listed are the rs ID for each SNP, the chromosome, 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 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 *.