Identification of key DNA methylation changes on fasting plasma glucose: a genome-wide DNA methylation analysis in Chinese monozygotic twins

Wang, Weijing; Yao, Wenqin; Tan, Qihua; Li, Shuxia; Duan, Haiping; Tian, Xiaocao; Xu, Chunsheng; Zhang, Dongfeng

doi:10.1186/s13098-023-01136-4

Table 3 The results of causal inference analysis of top CpGs with fasting plasma glucose

From: Identification of key DNA methylation changes on fasting plasma glucose: a genome-wide DNA methylation analysis in Chinese monozygotic twins

CpG No.	Chromosome	Position	HGNC symbol	Methylation to FPG					FPG to methylation
CpG No.	Chromosome	Position	HGNC symbol	β_{self_} _change	P_{self_} _change	β_{co-twin_} _change	P_{co-twin_} _change	Absolute value of ratio	β_{self_} _change	P_{self_} _change	β_{co-twin_} _change	P_{co-twin_} _change	Absolute value of ratio
1	chr12	105,478,501	ALDH1L2	0.016	4.63E−10	0.018	2.89E−10	1.065	− 0.500	3.13E−01	− 0.645	2.10E−01	1.290
2^b	chr17	27,052,829	TLCD1	0.017	2.03E−06	0.024	3.94E−05	1.421	− 0.329	5.35E−01	− 1.059	1.90E−02	3.218
3	chr19	658,314	RNF126	0.046	1.40E−03	0.068	1.86E−06	1.472	− 0.023	6.84E−01	− 0.170	1.56E−01	7.489
4	chr5	150,027,611	SYNPO	0.082	1.23E−03	0.105	2.20E−03	1.283	− 0.024	6.25E−01	− 0.049	2.60E−01	2.090
5^a	chr19	59,073,819	MZF1	0.029	3.96E−01	0.151	9.44E−03	5.230	0.018	7.19E−01	− 0.114	7.82E−02	− 6.429
6^a	chr7	157,670,224	PTPRN2	0.077	3.46E−06	0.150	2.03E−09	1.931	0.001	9.81E−01	− 0.072	1.12E−01	− 71.878
7^b	chr17	27,052,816	TLCD1	0.016	7.29E−05	0.023	5.30E−04	1.449	− 0.366	4.68E−01	− 1.077	1.80E−02	2.945
8	chr8	26,148,178	PPP2R2A	− 0.017	7.86E−05	−0.011	2.21E−03	0.618	0.630	1.23E−01	0.133	7.52E−01	0.212
9^a	chr19	59,073,806	MZF1	0.022	5.99E−01	0.112	4.71E−02	5.141	0.010	8.42E−01	− 0.080	1.76E−01	− 7.954
10	chr5	150,027,616	SYNPO	0.075	3.24E−03	0.095	4.41E−03	1.257	− 0.023	6.43E−01	− 0.044	3.23E−01	1.936
11^b	chr17	27,052,798	TLCD1	0.014	6.90E−04	0.019	2.95E−03	1.345	− 0.448	3.91E−01	− 0.963	4.57E−02	2.149
12	chr17	27,052,771	TLCD1	0.013	5.05E−03	0.015	1.54E−02	1.159	− 0.568	3.03E−01	− 0.797	1.41E−01	1.404
13^{a, b}	chr5	1,233,035	SLC6A18	0.140	7.45E−09	0.253	1.90E−09	1.808	0.005	8.90E−01	− 0.091	1.38E−02	− 18.774
14^{a, b}	chr5	1,233,066	SLC6A18	0.091	4.87E−06	0.177	2.09E−10	1.950	0.003	9.41E−01	− 0.070	3.82E−02	− 25.124
15^{a, b}	chr5	1,233,041	SLC6A18	0.134	8.86E−08	0.250	9.29E−09	1.862	0.008	8.17E−01	− 0.093	1.18E−02	− 11.256
16^{a, b}	chr5	1,233,045	SLC6A18	0.134	1.61E−07	0.249	1.14E−08	1.867	0.009	8.00E−01	− 0.092	1.09E−02	− 10.206
17^a	chr19	59,073,831	MZF1	0.025	4.45E−01	0.150	4.51E−03	6.074	0.024	6.57E−01	− 0.130	8.19E−02	− 5.416
18^b	chr9	119,332,867	ASTN2	0.154	2.04E−06	0.204	9.23E−08	1.331	− 0.044	4.75E−01	− 0.159	3.81E−03	3.636
19^b	chr9	119,332,835	ASTN2	0.091	1.65E−03	0.129	1.24E−05	1.425	− 0.047	4.56E−01	− 0.121	3.26E−02	2.598
20^a	chr7	157,670,239	PTPRN2	0.048	3.30E−03	0.162	5.31E−09	3.402	0.019	6.17E−01	− 0.070	1.01E−01	− 3.636
21	chr9	133,911,755	LAMC3	− 0.030	5.49E−01	0.088	1.59E−01	− 2.905	0.018	6.28E−01	− 0.029	3.65E−01	− 1.556
22^{a, b}	chr2	237,298,168	IQCA1	− 0.016	1.05E−06	−0.026	2.19E−07	1.626	0.0001	1.00E + 00	1.064	1.11E−02	7362.729
23^{a, b}	chr2	237,298,161	IQCA1	− 0.016	1.11E−06	−0.026	2.24E−07	1.628	− 0.003	9.95E−01	1.064	1.13E−02	− 407.723
24^a	chr3	129,059,046	NA	− 0.001	9.16E−01	−0.022	6.60E−03	41.613	− 0.326	4.63E−01	0.935	5.72E−02	− 2.869
25	chr5	29,364,034	LINC02064	0.044	3.14E−02	0.062	2.76E−03	1.419	− 0.030	6.24E−01	− 0.146	2.55E−01	4.921
26	chr10	126,490,028	FAM175B	− 0.036	6.57E−01	0.209	9.03E−02	− 5.886	0.010	7.41E−01	− 0.028	4.45E−01	− 2.713
27^a	chr9	140,033,560	GRIN1	0.029	2.49E−01	−0.047	4.72E−02	− 1.618	− 0.055	2.76E−01	0.064	1.29E−01	− 1.165
28	chr18	14,458,789	LONRF2P1	− 0.001	9.69E−01	−0.023	3.46E−01	18.309	− 0.027	8.78E−01	0.121	3.42E−01	− 4.420
29^a	chr5	1,233,018	SLC6A18	0.099	3.60E−04	0.193	3.06E−06	1.951	0.0003	9.93E−01	− 0.078	6.70E−02	− 223.473
30^{a, b}	chr11	72,352,936	PDE2A	0.143	1.95E−06	0.253	5.51E−10	1.770	− 0.006	8.45E−01	− 0.088	4.89E−03	14.239

Results in bold indicate the causation statistically significant
NA, not available; FPG, fasting plasma glucose
^aThe change of DNA methylation causes the FPG change
^bThe FPG change causes the change of DNA methylation

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ISSN: 1758-5996

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