Eight independent associations in seven genetic loci displayed genome-wide significant association with T2D-ESKD in the baseline or APOL1-negative models, including RND3/RBM43, SLITRK3, ENPP7, GNG7, APOL1, GRAMD3, and MGAT4C. In addition to APOL1, two genome-wide significant loci were associated with all-cause ESKD, EFNB2 and GNG7. Further, 10 genetic loci demonstrated nominal association with all-cause ESKD (P < 5 × 10−6), including LPP, FSTL5, OPRK1/ATP6V1H, SYBU/KCNV1, ALK/YPEL5, MNX1-AS1/UBE3C, NUP98, LINC01075/LINC00448, TMCO5A, and SULF2/LINC01522. Here, UBE3C is linked to type 2 diabetes mellitus.