Twenty-four rare SNPs, two HLA alleles (HLA-A*31:01 and HLA-B*07:05), and HLA-Baa-156R (P = 6.28 × 10−26, OR = 0.021) confer strong protective effects for NPC (Supplementary Table 13) and reached the genome-wide significance. This evidence concerns the gene HLA-A and nasopharyngeal carcinoma.