Considering each subtype, the highest HOXA9 promoter methylation frequency was found in oncocytomas (93%), followed by ccRCC (70%), chRCC (67%) and pRCC (60%), whereas the highest OXR1 promoter methylation frequency was found in pRCC (93%), followed by ccRCC and oncocytoma (87%), and then chRCC (80%). Here, HOXA9 is linked to nonpapillary renal cell carcinoma.