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Table 5 Genome-wide significant T2D-ESKD associations (P < 5 × 10−8) 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 Annotation Effect/other allele Stage 1a (1205 T2D-ESKD cases vs. 4669 non-diabetic non-nephropathy controls) Stage 1b (1377 T2D-ESKD cases vs. 657 non-diabetic non-nephropathy controls) Stage 1c (186 T2D-ESKD cases vs. 733 non-diabetic non-nephropathy controls) Stage 2: Meta-analysis (2768 T2D-ESKD cases vs. 6059 non-diabetic non-nephropathy controls)
EAF OR (95% CI) P Info EAF OR (95% CI) P Info EAF OR (95% CI) P Info EAF OR (95% CI) P HetP
rs75029938 5 125773333 GRAMD3 Intron T/C 0.044 2.27 (1.78,2.88) 1.88E−11 0.87 0.036 1.01 (0.62,1.65) 0.97 0.69 0.032 1.23 (0.51,2.96) 0.65 0.94 0.042 1.89 (1.54, 2.34) 2.02E−09 0.0094
rs17577888 12 87670213 MGAT4C Intergenic T/G 0.089 0.69 (0.58,0.82) 1.99E−05 1 0.086 0.59 (0.44,0.78) 0.00029 0.99 0.073 0.84 (0.46,1.55) 0.59 0.99 0.087 0.67 (0.58, 0.77) 3.87E−08 0.50
rs142671759 17 77706698 ENPP7 Intron C/T 0.025 2.71 (1.92,3.82) 1.46E−08 0.73 0.019 1.52 (0.78,2.94) 0.22 0.82 0.016 1.19 (0.39,3.7) 0.76 0.92 0.024 2.29 (1.7, 3.07) 4.1E−08 0.16
  1. APOL1-negative model: adjusted for age, sex, and PC1; APOL1 risk genotype carriers were excluded
  2. Abbreviations: T2D type 2 diabetes, ESKD end-stage kidney disease, CHR chromosome, POS position, N number, EAF effect allele frequency, OR odds ratio, CI confidence interval, P P value, Info imputation quality, HetP heterogeneity P value