Table 1 CpG sites with their methylation levels significantly associated with baseline eGFR or eGFR slope in the single-site analysis

From: DNA methylation markers for kidney function and progression of diabetic kidney disease

CpG site	Genomic ___location	Model coefficient	P value	Corrected P value	Annotated gene(s)	Gene region(s)
Baseline eGFR
cg17944885	Chr19:12,225,735	−5.156	1.41E-20	6.11E-15	–	–
cg25364972	Chr2:217,075,573	−6.303	4.36E-11	1.90E-05	–	–
cg06449934	Chr7:1,130,697	3.679	9.70E-11	4.22E-05	GPER	5’ UTR
					C7orf50	Gene body
cg02304370	Chr11:587,926	3.662	1.37E-10	5.97E-05	PHRF1	Gene body
cg21919729	Chr8:11,719,367	3.368	4.28E-10	1.86E-04	CTSB	5’ UTR
cg04610187	Chr17:76,360,794	3.766	5.83E-10	2.53E-04	–	–
cg04983687	Chr16:88,558,223	3.372	1.29E-09	5.61E-04	ZFPM1	Gene body
cg27254661	Chr2:73,118,624	3.697	2.47E-09	0.001	SPR	Gene body
cg18593194	Chr19:36,205,201	3.697	2.75E-09	0.001	ZBTB32	5’ UTR
cg12065228	Chr1:19,652,788	3.721	2.76E-09	0.001	PQLC2	Gene body
cg08940169	Chr16:88,540,241	3.260	4.16E-09	0.002	ZFPM1	Gene body
cg19434937	Chr12:7,104,184	3.206	4.16E-09	0.002	LPCAT3	Gene body
cg11699125	Chr1:6,341,327	3.144	6.55E-09	0.003	ACOT7	Gene body
cg17988187	Chr2:74,612,222	3.131	6.84E-09	0.003	LOC100189589	TSS1500
cg09823543	Chr6:43,146,056	3.557	7.10E-09	0.003	SRF	Gene body
cg02475695	Chr16:616,220	3.378	7.63E-09	0.003	NHLRC4	TSS1500
cg06972908	Chr16:30,488,321	4.344	8.35E-09	0.004	ITGAL	Gene body
cg11544657	Chr1:9,968,130	−4.430	8.61E-09	0.004	CTNNBIP1	5’ UTR
cg23845009	Chr11:34,323,678	4.360	1.09E-08	0.005	ABTB2	Gene body
cg09610644	Chr3:197,249,274	−3.469	1.26E-08	0.005	BDH1	Gene body
cg12981272	Chr3:37,281,848	5.063	1.36E-08	0.006	–	–
cg12077754	Chr2:75,089,669	3.114	1.38E-08	0.006	HK2	Gene body
cg10142874	Chr2:11,917,623	3.074	1.86E-08	0.008	LPIN1	Gene body
cg00934987	Chr17:56,605,468	3.540	2.68E-08	0.012	SEPT4	Gene body
cg22753611	Chr6:17,472,892	−3.284	2.68E-08	0.012	CAP2	Gene body
cg04816311	Chr7:1,066,650	4.226	2.88E-08	0.013	C7orf50	Gene body
cg04497992	Chr16:616,212	3.053	3.11E-08	0.014	NHLRC4	TSS1500
cg09249800	Chr1:6,341,287	3.042	3.15E-08	0.014	ACOT7	Gene body
cg01676795	Chr7:75,586,348	4.178	3.43E-08	0.015	POR	Gene body
cg25854298	Chr10:73,936,754	2.952	3.79E-08	0.016	ASCC1	Gene body
cg10489463	Chr2:33,546,572	3.190	4.07E-08	0.018	LTBP1	Gene body
cg23516680	Chr10:103,923,333	3.105	4.89E-08	0.021	NOLC1	3’ UTR
cg02170785	Chr14:69,650,830	3.012	5.44E-08	0.024	–	–
cg19448292	Chr20:35,504,064	3.177	5.59E-08	0.024	C20orf118	TSS1500
cg01499988	Chr9:35,755,346	2.980	6.16E-08	0.027	MSMP	TSS1500
cg25087851	Chr11:60,623,918	2.993	6.95E-08	0.030	GPR44	TSS1500
cg22406869	Chr11:66,276,941	4.239	7.63E-08	0.033	DPP3	3’ UTR
					BBS1	TSS1500
cg18650626	Chr7:1,914,073	2.886	8.89E-08	0.039	MAD1L1	Gene body
cg00506299	Chr3:16,469,127	3.373	9.14E-08	0.040	RFTN1	Gene body
cg16809457	Chr6:90,399,677	3.694	1.14E-07	0.050	MDN1	Gene body
eGFR slope
cg10272901	Chr21:46,677,879	1.316	7.84E-11	3.41E-05	–	–
cg12354056	Chr3:186,136,503	1.126	7.50E-10	3.26E-04	–	–
cg18461548	Chr8:37,701,921	1.179	2.72E-09	0.001	BRF2	3’ UTR
cg00695821	Chr3:156,124,891	1.354	3.81E-09	0.002	KCNAB1	Gene body
cg22822893	Chr6:15,1662,789	1.056	7.39E-09	0.003	AKAP12	Gene body
cg02566611	Chr16:83,948,975	0.986	5.61E-08	0.024	MLYCD	Gene body
cg20741134	Chr1:181,382,639	0.976	5.67E-08	0.025	–	–
cg04027328	Chr1:11,372,138	1.290	6.81E-08	0.030	–	–

P values were computed using two-sided Student’s t test. Each listed site has a Bonferroni-corrected P value <0.05. TSS1500: the region between 200 bp and 1500 bp upstream of the transcription start site (TSS). In the model coefficients, a positive sign means that a higher methylation level is associated with higher baseline eGFR or slower eGFR decline, while a negative sign means the opposite.

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Table 1 CpG sites with their methylation levels significantly associated with baseline eGFR or eGFR slope in the single-site analysis

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