Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome.

While the total number of nominally significant ( p < 0.05) correlations detected was slightly lower in AS analyses (27,324 versus 38,585 in MCC-Seq, 2927 versus 3274 in WGBS), AS analyses detected a higher rate of strong correlations when compared with NAS correlations for both MCC-Seq (Fig. 4a ) and WGBS (Fig. 4b ) across our datasets (Kolmogorov–Smirnov p value < 2.2 × 10 −16 for both WGBS and MCC-Seq).

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We further generated a list of high-confidence non-genetic CpG clusters by examining windows of at least 15 consecutive CpGs and selecting windows where all CpGs did not show significant genetic methylation (ASM and mQTL q ≥ 0.1) but showed significant imbalanced allelic methylation (GIT q < 1 × 10 −5 ), and where the median imbalanced allelic methylation was highly significant (log e ( q ) < −10) (Additional file 3 ).

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