The gene-based association analysis suggested four suggestively significant genes including SLC39A8, GOLGA8M, SMIM31and WHAMMP2. The gene-set-based association analysis prioritized three top genes (CDC45, NCOR1 and KAT2A), which have been implicated with HCC previously, mainly through regulated expression. This evidence concerns the gene GOLGA8M and hepatocellular carcinoma.