SNPs with UC GWAS P values < 1×10−4 were included on a list of replication genotyping candidates with priority scores for inclusion in the replication genotyping assigned according to significance of the association evidence. Among correlated (r2 > 0.5) SNPs with UC GWAS P values < 1×10−4, only the SNP with the most significant P value was chosen as the “best region” SNP and placed on the replication candidate list. Other replication genotyping candidates included a) SNPs at previously implicated CD or UC loci or their best UC GWAS proxies (r2 > 0.5 in a 1 Mb window of HapMap CEU data23 centered on the implicated SNP) that showed nominal evidence for association (P < 0.05) in our UC GWAS, and b) previously implicated SNPs that did not have a proxy in our UC GWAS. Finally, additional SNPs from loci that demonstrated genome-wide significant evidence for association were added to the replication candidate list. rs6426833, rs2395185 and rs1558744 were genotyped by Pyrosequencing (Biotage AB, Uppsala, Sweden) at the University of Pittsburgh. SNPs on the replication candidate list that had designable
