Due to increased power compared to previous GWA studies, we identified genetic variants including in TP53 and STING1 and validated known variants in BRCA2 separately in LA and HPC, two under-studied cancer sites, as well as multiple signals in HPC, such as GDF7. Variants from fine mapping highlight key differences in HLA associations between HPV(+) OPCs, HPV(-) OPCs and OCs. Here, BRCA2 is linked to cancer.