We found that two functional SNPs (PANX1 rs3020013 A > G and APP rs9976425 C > T) were significantly associated with HBV-related HCC OS with the adjusted hazard ratio (HR) of 0.83 [95% confidence interval (CI) = 0.73–0.95, P = 0.008], and 1.26 (95% CI = 1.02–1.55, P = 0.033), respectively. The gene discussed is APP; the disease is hepatocellular carcinoma.