These findings suggested that the PHF3-PTP4A1 region might harbor a causal locus and that the proteins encoded by PHF3 and PTP4A1 might contribute to the vulnerability to alcohol dependence. First, the risk LD block in the region of PHF3-PTP4A1 formed the only association peak within a 90 Mb region in AAs (threshold p = 10−4) and within a 10 Mb region in EAs (threshold p = 1.5×10−3). It is, thus, highly likely that the putative causal locus for alcohol dependence was located within this PHF3-PTP4A1 LD block. We speculated that there might be only one causal locus in this region, and all risk SNPs might be in LD with this putative causal locus and, thus, presented association signals. If there were ≥2 independent causal loci, the risk markers in LD with respective causal loci would be located in ≥2 independent risk LD blocks, which were not observed in the present study. Second, most replicable risk SNPs in this block had strong cis-acting regulatory effects on PHF3-PTP4A1 mRNA expression. This increased the possibility that PHF3-PTP4A1 per se played a direct functional
