When HLA-A*11:01 is the index allele, the extreme NPC association signal is diminished to 0.1–0.01 by HLA-A aa variants as well as each SNP in the genes adjacent to HLA-A locus (See Figure 3B and HLA-A*11:01 column in Table S11). Here, HLA-A is linked to nasopharyngeal carcinoma.