Table 3.

The association of the 48 differentially methylated CpG sites with CIR, BMI and diabetes risk in later life

CpG	Gene/CpG island	CIR			BMI			Diabetes risk
		Effect (SD/SD)	95% CI	p value	Effect (%/SD)	95% CI	p value	HR (/SD)	95% CI	p value
cg24049468	AK3	−0.088	−0.162, −0.013	0.02*	0.9	−2.1, 4.0	5.7 × 10−1	1.13	0.82, 1.45	0.44
cg25949304	PCDHGA4	0.080	0.010, 0.150	0.03*	−3.0	−5.7, −0.3	3.1 × 10−2*	0.93	0.66, 1.21	0.63
cg04645534	STC1	0.072	0.002, 0.141	0.05*	−4.5	−7.2, −1.8	1.3 × 10−3*	0.97	0.67, 1.27	0.85
cg16426215	chr16:56709677–56709953	0.123	−0.004, 0.249	0.06	−2.9	−7.6, 2.0	2.4 × 10−1	0.95	0.40, 1.49	0.84
cg09674170	CLDN9	−0.076	−0.161, 0.008	0.08	1.0	−2.4, 4.5	5.6 × 10−1	1.18	0.70, 1.32	0.39
cg06717221	ATP8B3	−0.065	−0.137, 0.007	0.08	−3.1	−5.9, −0.3	3.2 × 10−2*	1.01	0.81, 1.56	0.94
cg12140144	PRDM16	0.074	−0.015, 0.163	0.10	6.0	2.4, 9.8	1.2 × 10−3*	2.12	1.74, 2.50	9.7 × 10−5*
cg20941258	TDGF1	0.053	−0.033, 0.139	0.23	2.6	−0.8, 6.2	1.3 × 10−1	1.37	1.01, 1.73	0.08
cg24996440	chr2:3583550–3584833	0.049	−0.039, 0.137	0.28	−3.0	−6.3, 0.5	8.9 × 10−2	0.85	0.49, 1.20	0.36
cg17186803	SCN4B	0.058	−0.050, 0.166	0.29	6.2	1.5, 10.7	8.9 × 10−3*	1.25	0.77, 1.72	0.37
cg08911291	chr9:44118137–44120175	0.044	−0.041, 0.129	0.31	3.3	−0.1, 6.8	5.5 × 10−2	1.47	1.09, 1.85	0.05*
cg07464358	-	−0.062	−0.184, 0.060	0.32	9.2	4.3, 14.4	2.3 × 10−4*	1.21	0.71, 1.71	0.45
cg20769177	WNT9B	0.031	−0.038, 0.101	0.38	−0.7	−3.3, 2.0	6.0 × 10−1	1.11	0.77, 1.45	0.55
cg05772155	chr10:65800729–65801528	−0.029	−0.096, 0.038	0.40	−1.6	−4.1, 1.0	2.2 × 10−1	0.94	0.68, 1.19	0.62
cg10772621	chr19:54411376–54411968	0.029	−0.041, 0.100	0.41	−4.9	−7.4, −2.4	2.3 × 10−4*	0.98	0.69, 1.27	0.89
cg07993743	WNT9B	0.027	−0.042, 0.097	0.44	−1.0	−3.7, 1.8	5.0 × 10−1	1.02	0.70, 1.35	0.89
cg15618978	TRIM59	0.030	−0.055, 0.116	0.49	2.5	−1.1, 6.3	1.7 × 10−1	0.99	0.61, 1.37	0.96
cg04350311	ELFN2	0.027	−0.052, 0.106	0.51	4.2	1.1, 7.5	9.2 × 10−3*	0.94	0.59, 1.29	0.73
cg03862414	PLEKHH3	−0.026	−0.105, 0.053	0.52	1.5	−1.7, 4.8	3.7 × 10−1	1.07	0.76, 1.43	0.71
cg15833797	LHX3	−0.025	−0.102, 0.052	0.52	0.1	−2.9, 3.2	9.5 × 10−1	1.09	0.72, 1.41	0.61
cg14381623	LHX3	0.021	−0.045, 0.087	0.53	2.0	−0.7, 4.7	1.6 × 10−1	1.07	0.78, 1.37	0.64
cg08414676	SORD	−0.023	−0.097, 0.052	0.55	−1.3	−4.1, 1.6	3.7 × 10−1	1.01	0.71, 1.32	0.93
cg08370430	chr17:12927455–12928747	−0.021	−0.097, 0.056	0.60	−1.1	−4.1, 1.9	4.6 × 10−1	0.98	0.67, 1.30	0.91
cg04413090	SBK1	0.018	−0.054, 0.091	0.62	5.3	2.4, 8.4	4.1 × 10−4*	1.08	0.78, 1.38	0.62
cg20345234	chr10:65800729–65801528	−0.017	−0.086, 0.052	0.63	−2.3	−4.9, 0.3	8.7 × 10−2	0.99	0.70, 1.28	0.96
cg16482344	LINC00839	0.017	−0.052, 0.086	0.63	−1.7	−4.3, 1.0	2.1 × 10−1	0.96	0.69, 1.23	0.77
cg24503407	PM20D1	0.017	−0.055, 0.090	0.64	−1.0	−3.6, 1.7	4.8 × 10−1	0.99	0.69, 1.29	0.94
cg21192468	LHX3	−0.013	−0.077, 0.051	0.69	2.3	−0.4, 5.0	9.5 × 10−2	1.04	0.76, 1.32	0.79
cg26671988	chr5:102090439–102091241	−0.015	−0.092, 0.063	0.71	1.2	−1.9, 4.5	4.5 × 10−1	1.17	0.84, 1.50	0.35
cg27073142	SORD	−0.012	−0.080, 0.056	0.73	−1.7	−4.2, 0.9	2.1 × 10−1	1.10	0.81, 1.42	0.52
cg25629768	LMNB2	−0.014	−0.097, 0.068	0.73	1.3	−1.9, 4.5	4.4 × 10−1	1.13	0.79, 1.46	0.49
cg15183961	ANKRD20A2	−0.014	−0.097, 0.068	0.73	4.4	1.4, 7.6	4.4 × 10−3*	1.12	0.82, 1.38	0.47
cg12875241	GPR143	0.011	−0.056, 0.079	0.74	0.7	−2.0, 3.4	6.2 × 10−1	1.03	0.74, 1.31	0.87
cg20749955	PPP1R3B	0.012	−0.060, 0.084	0.75	−4.0	−6.6, −1.2	4.7 × 10−3*	0.96	0.64, 1.28	0.81
cg08292290	GLRX5	0.013	−0.072, 0.098	0.76	−3.5	−6.4, −0.5	2.2 × 10−2*	1.09	0.73, 1.45	0.65
cg25952247	LHX3	0.009	−0.056, 0.074	0.78	−0.2	−2.9, 2.5	8.6 × 10−1	0.97	0.69, 1.25	0.83
cg14105781	TBL1X	−0.019	−0.154, 0.117	0.79	3.9	−1.4, 9.4	1.5 × 10−1	0.91	0.11, 1.21	0.75
cg00509616	GCOM1	−0.012	−0.097, 0.074	0.79	3.9	0.6, 7.5	2.3 × 10−2*	1.25	0.87, 1.64	0.25
cg27222147	CACNA1C	0.018	−0.113, 0.149	0.79	−3.0	−7.5, 1.7	2.1 × 10−1	0.66	0.38, 1.45	0.14
cg06268875	PIEZ02	0.008	−0.066, 0.083	0.82	−1.2	−3.9, 1.6	3.9 × 10−1	0.93	0.63, 1.23	0.65
cg14732789	chr20:29534910–29535208	−0.009	−0.096, 0.078	0.84	−3.7	−7.0, −0.4	2.9 × 10−2*	1.30	0.95, 1.64	0.14
cg21172615	LHX3	−0.007	−0.082, 0.068	0.86	2.5	−0.5, 5.6	1.1 × 10−1	1.01	0.66, 1.36	0.94
cg14605520	LHX3	0.005	−0.071, 0.080	0.90	0.7	−2.2, 3.7	6.4 × 10−1	1.03	0.70, 1.36	0.86
cg05806645	PPP1R3B	0.004	−0.066, 0.073	0.91	−2.8	−5.4, 0.0	5.0 × 10−2*	1.18	0.85, 1.50	0.33
cg13700073	FSCN2	−0.004	−0.080, 0073	0.93	−2.3	−5.4, 0.8	1.4 × 10−1	0.97	0.63, 1.31	0.86
cg13427473	-	0.002	−0.078, 0.081	0.97	−3.6	−6.4, −0.6	1.9 × 10−2*	1.02	0.69, 1.35	0.91
cg00762450	ANKRD20A4	−0.001	−0.081, 0.078	0.97	3.5	0.4, 6.8	2.8 × 10−2*	1.26	0.93, 1.59	0.17
cg15796459	SHROOM2	−0.001	−0.12.6, 0.125	0.99	−2.9	−7.4, 1.7	2.2 × 10−1	1.69	1.16, 2.21	0.05

CpG position is given in a chromosome:base pair format

A CpG is assigned to a gene if it is located within the gene region; if it is not within a gene region, the start/stop of the CpG island is given

The effect size of CIR is shown as the SD difference in CIR per SD difference in M-value. The effect size of BMI is shown as the per cent difference in BMI (expressed as a multiplier) per SD of M-value.

The HR for development of diabetes is shown per SD of M-value. The 95% CI of effects/HRs are shown in the adjacent columns

All associations were adjusted for age, sex and proportion of the American Indian ancestry of the offspring, as well as for the mother’s age when the child was born, array batch and four PCs (the four most significant PCs were calculated from genome-wide methylation data). CIR was additionally adjusted for BMI and HOMA-IR of the offspring. All the models were further corrected for intrauterine exposure to diabetes

^*p ≤ 0.05