Table 5.

Genome-wide significant T2D-ESKD associations (P < 5 × 10⁻⁸) in APOL1-negative model

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

APOL1-negative model: adjusted for age, sex, and PC1; APOL1 risk genotype carriers were excluded

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