Table 3. External datasets considered in this analysis.

CpG set	Notes
Putative metastable epialleles (MEs)	1881 ME/SIV/ESS CpGs overlapping array background identified in multi-tissue and MZ/DZ screens in Van Baak et al., 2018 and Kessler et al., 2018.
Parent-of-origin-specific methylation (PofOm)	699 Parent-of-origin-specific methylation loci identified in peripheral blood in Zink et al., 2018, overlapping array background.
Embryo DNAm data	RRBS data for inner cell mass and embryonic liver (<10 weeks’ gestation) from Guo et al., 2014.
Sperm DNAm data	WGBS data from Okae et al., 2014.
Germline DMRs (gDMRs)	Regions differentially methylated in sperm and oocytes identified in WGBS data by Sanchez-Delgado et al., 2016.
Transposons (ERVs)	ERVs determined by RepeatMasker were downloaded from the UCSC h19 annotations repository.
Transcription factor ChIP-seq	ZFP57, TRIM28, and CTCF transcription factor binding sites identified from ChIP-seq in human embryonic kidney and hESCs are described in Kessler et al., 2018.
Chromatin state predictions and histone three marks	Chromatin state predictions for H1 ESCs, fetal brain, fetal muscle, and fetal small intestine generated using Ernst and Kellis, 2012, from Roadmap Epigenomics Consortium et al., 2015. Histone mark data are from the same source.

ME: metastable epiallele; SIV: systemic interindividual variation; ESS: epigenetic supersimilarity; MZ/DZ: monozygotic/dizygotic twins; PofOm: parent-of-origin methylation; RRBS: reduced representation bisulfite-seq; DMR: differentially methylated region; ERV: endogenous retrovirus; ESCs: embryonic stem cells. See materials and methods for further details.