In a recent genome-wide association study (GWAS), we identified a unique novel, functional and replicable risk genomic region for alcohol dependence. This region (Chr6: 64,066,604-64,831,120) included the protein tyrosine phosphatase type IVA 1 gene (PTP4A1), the plant homeodomain finger protein 3 gene (PHF3) and part of the eyes shut homolog gene (EYS). It was enriched with numerous replicable common risk variants (minor allele frequency (MAF) >0.05) for alcohol dependence across African–Americans, European–Americans and European–Australians. Within 90 Mb range surrounding this region in the discovery sample, all variants with P<10−4 were concentrated in this region. Most of these risk variants had significant cis-acting regulatory effects on mRNA expression. The distributions of −log(P) values for association and functional signals in this region were highly consistent across six independent populations. We thus speculated that this region might harbor a causal variant(s) for alcohol dependence.1