Cis-eQTL analysis showed that 24 of the 30 replicable risk SNPs had significant cis-acting regulatory effects on PHF3-PTP4A1 mRNA expression level in at least one of HapMap CEU-Children, CEU-Parent and CHB populations ( Table 1 ; Figure 1D–F ), and 12 of them survived region-wide correction (α = 0.01). PHF3-PTP4A1 was enriched with many other functional signals across five HapMap populations ( Figure 1 ), although these functional SNPs in JPT and YRI-Parent were not exactly, but in high LD with, those replicable risk SNPs in the AA discovery sample ( Figure 1G–H ).
