Table 3.

Results of AYATS Enrichment Analyses.^a

Annotation	cis		trans
	Enriched	Depleted	Enriched	Depleted
Chromatin Statesb	TxFlnk (3), ZNF/Rpts (8)	Tx (4), TxWk (5), Quies (15)	TssAFlnk(2), TxFlnk (3), TxWk (5), EnhG (6), Enh (7)	TssA (1) Het (9), TssBiv (10), BivFlnk (11), ReprPC (13), ReprPCWk (14)
CpG Classifiers	South Shore	North shore, Island	South shore, Open sea	North shelf, North shore, Island
Gene Regions		5’-UTRs, Promoters	Introns	5’-UTRs, Promoters
Otherc	Enhancers, TF binding	lncRNAs	Enhancers	lncRNAs, Insulators

Abbreviations. UTR = untranslated region; TF = transcription factor; lncRNAs = long non-coding RNAs.

Bolded items. P-value <0.0025 (Bonferroni corrected for 20 tests)

Underlined items. Concordance across both the AYATS and PREG study.

^aP-value < 0.05.

^bENCODE ChromHMM 15-state model; 1 = Active transcriptional start site (TSS), 2 = Flanking active TSS, 3 = Flanking strong transcription, 4 = Strong transcription, 5 = Weak transcription, 6 = Genic enhancer, 7 = Active enhancer, 8 = Zinc-finger genes and repeats, 9 = Heterochromatin, 10 = Bivalent/poised TSS, 11 = Flanking bivalent TSS, 12 = Bivalent Enhancers, 13 = Polycomb-repressed, 14 = Weak Repressed Polycomb, 15 = Quiescent.

^cFANTOM5-defined enhancers, transcription factor binding sites derived from ENCODE TF ChIP-seq, GENCODE long non-coding RNAs.