The methylation status of GREM1 (region i), LAD1 (region i and ii), NEFH (region i), NEURL (region ii), SFRP1, and GATA5 was significantly associated with poorer ccRCC-specific survival (log-rank test, P ≤ 0.0001–0.0117, Additional file 1: Fig. S7). Here, GATA5 is linked to nonpapillary renal cell carcinoma.