Table 4.

Results of PREG Enrichment Analyses.^a

Annotation	cis			trans
	Enriched	Depleted	Enriched	Depleted
Chromatin Statesb	TssA (1), ZNF/Rpts (8)	TssAFlnk (2), Tx (4)	TssAFlnk(2), TxFlnk (3), Enh (7), EnhBiv (12)	TxWk (5), Het (9), ReprPCWk (14),Quies (15)
CpG Classifiers	South Shore		North shore, South shore	Island
Gene Regions			Exons	Promoters, 3’-UTRs
Otherc	TF binding		Enhancers, TF binding

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 = Flank- ing active TSS, 3 = Flanking strong transcription, 4 = Strong transcription, 5 = Weak tran- scription, 6 = Genic enhancer, 7 = Active enhancer, 8 = Zinc-finger genes & repeats, 9 = Heterochromatin, 10 = Bivalent/poised TSS, 11 = Flanking bivalent TSS, 12 = Bivalent En- hancers, 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.