Here, two independent case-control studies were conducted—phase I cohort with 350 NPC cases and 619 controls and phase II cohort with 816 NPC cases and 1721 controls to determine if the polymorphisms of ITGA9, HLA-A, HLA-F, GABBR1, and HCG9 were associated with NPC development or can be potential genetic markers for onset of NPC in a Southern Chinese population. Here, GABBR1 is linked to nasopharyngeal carcinoma.