Table 6.

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

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

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;

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