A reported GWAS SNP was considered to coincide with an eQTL identified during the conditional analysis of cis associations if the GWAS SNP itself or any SNPs with r2 > 0.8 with this SNP were part of one of the eQTL peaks (P < 5 × 10−8). Enrichment of peak eQTLs for individual GWAS categories, as well as overall enrichment of GWAS SNPs, was tested with Fisher’s exact test by comparing the overlap obtained for peak eQTLs to that observed for all SNPs tested for cis associations. Publicly available summary statistics for a 200-kb window around CARD9 from the latest CD GWAS meta-analysis (46) were extracted using the Ricopili tool (www.broadinstitute.org/mpg/ricopili/). LD calculations were performed with PLINK (54) and the phase 1 1000 Genomes data (63). Approximate conditional analysis, based on summary statistics and LD properties, was carried out using the method described in (46).
