This study now provides important novel insights of putative functional SNPs disrupting transcription factor binding, altering target gene transcription for NPC pathogenesis, highlighting the possible involvement of E3 ubiquitin ligases, TRIM31, TRIM39, and TRIM39-RPP21 fusion protein impacting the host innate immunity antiviral defense and for this EBV-associated cancer. Here, TRIM31 is linked to nasopharyngeal carcinoma.