Thirty-two SNPs of the 74 unimputed risk markers, including 16 replicable SNPs, had functional cis-eQTL signals in at least one of the three HapMap populations (CHB, JPT and YRI-Parent) and the two European samples (0.003≤p≤0.044 for gene-level expression and 1.4×10−4≤p≤0.006 for exon-level expression; Table 3). There were other non-risk markers in this region that had significant cis-eQTL signals too (3.0×10−4≤p≤0.049 for gene-level expression and 4.2×10−7≤p≤0.001 for exon-level expression; Table S312). Additionally, many of the risk markers also had nominal trans-acting regulatory effects, which, however, were not significant after Bonferroni correction (data not shown).
