In conclusion, we identified three potentially functional SNPs (NEURL1B rs4868192 T>C, CNTN1 rs444927 G>A, and FCER2 rs1990975 C>T), which were significantly associated with HBV‐related HCC OS, likely by regulating the mRNA expression of the corresponding genes. This evidence concerns the gene CNTN1 and hepatocellular carcinoma.