In order to determine whether our newly derived functional score can aid in identifying associations likely to be replicated, we first examined the summary data for Crohn's disease from the WTCCC association study [11] (downloaded when results data were publicly available). After QC (less than 5% missing data, good clustering), we filtered SNPs at a 1% MAF threshold, and removed markers with no rs ID, leaving 391,878 SNPs. We matched these SNPs using the rs IDs within the SCAN database, leaving us with 386,306 SNPs.
