Table 1 Top 10 CpGs associated with MHC and MSS

CpG ID	Chr	Position	P	Beta	SE	Gene Symbol	Relation to CpG Island
MHC
cg07515565	6	1624386	6.6 × 10⁻¹²	−0.00382	0.000556	GMDS	Island
cg12453228	6	41338345	7.8 × 10⁻¹⁰	−0.00467	0.00076		N_Shore
cg15233611	12	122244660	2.2 × 10⁻⁹	−0.0048	0.000802	SETD1B	S_Shore
cg03025830	8	21905599	8.1 × 10⁻⁹	−0.00842	0.001461	FGF17	Island
cg13851767	9	123656764	2.9 × 10⁻⁸	−0.00492	0.000887		Island
cg24724428	6	11044888	4.2 × 10⁻⁸	0.003733	0.000681	ELOVL2	Island
cg11613559	10	121577971	6.3 × 10⁻⁸	−0.00399	0.000738	INPP5F	Island
cg19969694	15	41185800	6.5 × 10⁻⁸	−0.0031	0.000573	VPS18	N_Shore
cg19234738	3	134031551	6.7 × 10⁻⁸	−0.00494	0.000915		N_Shore
cg18964375	1	33772147	8.0 × 10⁻⁸	−0.00406	0.000757		Island
MSS
cg02454536	15	68713677	7.2 × 10⁻¹⁵	−0.02016	0.002591	ITGA11
cg12559228	19	50191882	4.5 × 10⁻¹¹	−0.00894	0.001357	C19orf76	N_Shore
cg14818812	8	142362180	6.6 × 10⁻¹¹	−0.01232	0.001887
cg16879115	12	7819180	9.7 × 10⁻¹¹	−0.00798	0.001233	APOBEC1
cg15233611	12	122244660	2.2 × 10⁻¹⁰	−0.01431	0.002255	SETD1B	S_Shore
cg27363141	6	30038929	4.0 × 10⁻¹⁰	−0.00407	0.000651	RNF39	Island
cg19254163	11	60623782	4.1 × 10⁻¹⁰	−0.00975	0.00156	GPR44	S_Shelf
cg07843568	19	1254066	6.2 × 10⁻¹⁰	−0.00841	0.00136	MIDN	Island
cg10498052	17	16367232	1.7 × 10⁻⁹	−0.00803	0.001332	NCRNA00188
cg11386711	3	186651116	2.2 × 10⁻⁹	−0.01106	0.001848	ST6GAL1	S_Shelf

MHC mitochondrial heteroplasmy count score, MSS mitochondrial local constraint score sum. Relation to CpG Island, Relation to UCSC CpG Island (see Supplementary Data 6–7). Genome-wide association analyses were performed between DNA methylation and heteroplasmy measures (MHC and MSS) using linear regression. Association significance was assessed using a two-sided t-test. A false discovery rate (FDR) threshold of p < 0.05, corresponding to p < 0.0000253 for MHC and p < 0.0000735 for MSS, was applied to determine significance. Gene names were italicized.

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