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Table 6 All-cause ESKD-associated variants at P < 5 × 10−6 in APOL1-negative model

From: Genome-wide association study identifies novel loci for type 2 diabetes-attributed end-stage kidney disease in African Americans

Lead variant CHR POS Locus Effect/other allele *Info Stage 2: Meta-analysis (2768 T2D-ESKD cases vs. 6059 non-diabetic non-nephropathy controls) Stage 4 (1019 non-diabetic ESKD cases vs. 733 non-diabetic non-nephropathy controls) Stage 5 (3787 all-cause ESKD cases vs. 6059 non-diabetic non-nephropathy controls)
EAF OR (95% CI) P EAF OR(95% CI) P EAF OR (95% CI) P HetP
rs12472637 2 30304514 ALK/YPEL5 A/G 0.94 0.33 0.81 (0.74, 0.89) 6.05E−06 0.36 0.8 (0.66, 0.96) 0.019 0.33 0.82 (0.76, 0.89) 4.47E−06 0.83
rs76971802 3 188607071 LPP T/C 0.95 0.09 1.43 (1.24, 1.65) 1.06E−06 0.08 1.45 (1.03, 2.05) 0.032 0.088 1.42 (1.24, 1.62) 5.76E−07 0.93
rs6459733 7 156930550 MNX1-AS1/UBE3C G/C 0.97 0.39 1.25 (1.15, 0.87) 1.32E−07 0.39 1.25 (1.03, 1.53) 0.026 0.39 1.24 (1.15, 1.35) 7.17E−08 0.83
rs4910809 11 3813850 NUP98 C/G 0.98 0.02 0.53 (0.4, 0.7) 9.46E−06 0.02 0.53 (0.29, 0.95) 0.034 0.023 0.53 (0.41, 0.69) 2.12E−06 0.63
rs219020 13 63013622 LINC01075/LINC00448 C/T 0.97 0.14 1.31 (1.17, 0.86) 6.84E−06 0.11 1.38 (1.02, 1.87) 0.037 0.14 1.31 (1.17, 1.47) 2.12E−06 0.58
rs113452507 15 37954309 TMCO5A C/G 0.92 0.16 1.29 (1.15, 1.45) 9.71E−06 0.16 1.38 (1.07, 1.77) 0.014 0.16 1.31 (1.18, 1.45) 8.48E−07 0.93
rs373971520 19 2568805 GNG7 –/CA 0.81 0.11 1.47 (1.28, 1.7) 8.97E−08 0.11 1.39 (1.01, 1.91) 0.044 0.11 1.46 (1.28, 1.67) 2.17E−08 0.016
rs6094913 20 46561443 SULF2/LINC01522 G/A 0.93 0.09 0.72 (0.63, 1.6) 8.28E−06 0.10 0.67 (0.48, 0.91) 0.012 0.092 0.72 (0.63, 0.83) 2.5E−06 0.70
  1. Abbreviations: T2D type 2 diabetes, ESKD end-stage kidney disease, CHR chromosome, POS position, EAF effect allele frequency, OR odds ratio, CI confidence interval, P P value, *Info imputation quality, HetP heterogeneity P value;
  2. APOL1-negative model: adjusted for age, sex, and PC1; APOL1 risk genotype carriers were excluded