Table 2.

Associations of MSI2, RAPH1 and SLC25A10 DNA methylation with anthropometry Associations of MSI2, RAPH1 and SLC25A10 DNA methylation with anthropometrical measures of adiposity (BMI, waist, skin folds) at ages 17 and 20 years and associations with measures of body composition (subcutaneous and visceral fat thickness at age 17 years, and DEXA measurements at age 20 years). All models were adjusted for age, sex and where available for cell count (CD4, CD8, NK, B Cell, Monocytes). Covariates with high variance inflation factors were removed to avoid collinearity as well as Granulocytes. All β-coefficients are expressed per SD change of CpG. q-values which pass FDR accounting for multiple testing are shown in darker font. ^# Log transformed.

			17 Year old					20 Year old
Outcome	Gene	CpG	β	P-Value	FDR (q-value)			β	P-Value	FDR (q-value)
Anthropometry
BMI#	MSI2	CpG1	0.027	2.5 x 10−4	0.003			0.026	4.0 x 10−4	0.003
		CpG2	0.026	1.3 x 10−4	0.002			0.027	3 x 10−4	0.003
		CpG3	0.032	0.001	0.004			0.027	3 x 10−4	0.003
	SLC25A10	CpG1	0.020	0.011	0.028			0.015	0.041	0.068
		CpG2	0.030	1.4 x 10−4	0.002			0.016	0.028	0.051
	RAPH1		0.013	0.102	0.157
Waist#	MSI2	CpG1	0.020	4.3 x 10−4	0.003			0.018	0.002	0.006
		CpG2	0.019	2.1 x 10−4	0.003			0.024	0.000	0.000
		CpG3	0.028	1.6 x 10−4	0.002			0.014	0.017	0.037
	SLC25A10	CpG1	0.009	0.126	0.177			0.014	0.017	0.037
		CpG2	0.018	0.004	0.012			0.012	0.035	0.061
	RAPH1		−0.001	0.893	0.922
Skinfolds
Suprailiac#	MSI2	CpG1	0.070	0.004	0.012			0.050	0.018	0.038
		CpG2	0.075	4.7 x 10−4	0.003			0.067	0.001	0.006
		CpG3	0.080	0.007	0.018			0.058	0.007	0.018
	SLC25A10	CpG1	0.020	0.406	0.488			0.058	0.007	0.018
		CpG2	0.024	0.444	0.514			0.044	0.037	0.063
	RAPH1		−0.023	0.345	0.426
Subscapular#	MSI2	CpG1	0.060	0.001	0.004			0.052	0.001	0.006
		CpG2	0.056	0.001	0.004			0.052	0.001	0.006
		CpG3	0.071	0.002	0.007			0.039	0.018	0.038
	SLC25A10	CpG1	0.023	0.219	0.285			0.029	0.083	0.133
		CpG2	0.029	0.158	0.218			0.027	0.102	0.157
	RAPH1		−0.012	0.522	0.583
Triceps#	MSI2	CpG1	0.055	0.003	0.001			0.023	0.189	0.253
		CpG2	0.056	0.001	0.004			0.037	0.033	0.058
		CpG3	0.050	0.026	0.049			0.014	0.403	0.488
	SLC25A10	CpG1	0.028	0.127	0.177			0.040	0.021	0.043
		CpG2	0.056	0.017	0.038			0.039	0.022	0.044
	RAPH1		−0.002	0.923	0.937
Measures of body composition
Subcutaneous fat#	MSI2	CpG1	0.082	0.001	0.004
		CpG2	0.068	0.003	0.001
		CpG3	0.028	1.6 x 10−4	0.002
	SLC25A10	CpG1	0.080	0.004	0.012
		CpG2	0.087	0.003	0.001
	RAPH1		0.015	0.577	0.630
Visceral fat#	MSI2	CpG1	0.013	0.443	0.514
		CpG2	−0.016	0.322	0.402
		CpG3	−0.039	0.451	0.516
	SLC25A10	CpG1	0.011	0.548	0.605
		CpG2	0.000	0.985	0.985
	RAPH1		−0.039	0.122	0.176
Lean Mass#	MSI2	CpG1						0.013	0.016	0.037
		CpG2						0.013	0.014	0.034
		CpG3						0.019	4.0 x 10−4	0.003
	SLC25A10	CpG1						−0.009	0.110	0.160
		CpG2						−0.002	0.690	0.728
	RAPH1							0.014	0.026	0.046
Fat mass#	MSI2	CpG1						0.026	0.176	0.238
		CpG2						0.043	0.026	0.049
		CpG3						0.022	0.267	0.343
	SLC25A10	CpG1						0.043	0.029	0.053
		CpG2						0.031	0.108	0.160
	RAPH1							0.013	0.533	0.601