Suplemental_methods.docx, Supplemental_tables.xlsx
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	- Main supplemental methods/tables for the manuscript.


singularity_container.sif, singularity_container_definition.txt:
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	- Singularity container and definition files used for training CNN models with Keras.


models_trained.tar.gz:
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	- CNN_models/
		Trained CNN models
	- lsgkm_models/
		LG-GKM SVM models trained on DNA sequences.
	- feature_models/
		Models trained on sequence features (CG, GC, CpG, CGI).
		SVM model files are SVM.*
		Logistic regression files are LogReg.*


supplemental_files.tar.gz:
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	- ENCFF050EKS.bedpe.hg19.gz
		ENCODE Hi-C chromatin loop file for HepG2

	- FitHiChIP.interactions_FitHiC_Q0.0001.hg19.bed.gz
		Long-range chromatin contacts generated using FitHiChIP program for HepG2

	- GWAS_enrichments.p_adj.txt.gz, GWAS_enrichments.txt.gz
		GWAS traits enriched in HepG2 HOT loci based on adjusted and unadjusted p-values

	- HOTs_with_common_tfs/
		HOT loci generated by applying our definition using only DAPs for which ChIP-seq datasets are available in all three cell lines (HepG2, K562 and H1)

	- HOTs_with_subsampled_to_H1/
		HOT loci generated by applying our definition using DAPs randomly subsampled to the number of H1 DAPs

	- HepG2_enhancers_DHS_H3K27ac.bed.gz, HepG2_enhancers_DHS_H3K27ac.bed.vertebrate.phastcons.gz, K562_enhancers_DHS_H3K27ac.bed.gz
		phastCons conservation scores and enhnacer regions in HepG2 and K562 defined using DHS regions and H3K27ac. Referred to as "regular enhancers" in the text.

	- HepG2_superenhancers.bed.gz
		super-enhancer regions in HepG2

	- Housekeeping_GenesHuman.csv
		List of housekeeping genes.

	- TF_binwise_signal_values.txt
		ChIP-seq signal values in loci binned by number of bound DAPs.

	- chipseq_signal_values_by_tfs.csv.gz
		ChIP-seq signal values of individual DAPs in HOT loci.

	- Tau_gene_V8.csv.gz
		Tau metrics of genes measuring the tissue-specificities of their expressions.

	- all_dhs_merged.bed.gz
		Globally merged DHS regions of all available DHS datasets of ENCODE. Used as a background when necessary/

	- classification_results.txt
		AUC values of calssification experiments.

	- hg19_files/
		Various annotation files of hg19 genomes (promoters, exons, CpG islands etc.) downloaded from UCAS Genome Browser database.

	- human_transcription_factors.txt
		Catalogue of annotations of transcription factors, used for analyzing seqquence-specific and non-sequence-specific DAPs.

	- metadata_HepG2_K569_H1.txt
		Metadata of ENCODE datasets used in the study.

	- peaks/
		ChIP-seq peaks files lifted over to hg19.

	- singularity_container.sif, singularity_container_definition.txt
		Singularity container (and definition file) used for running deep learning models.

	- tf_stats_summary_table.txt
		summary statistics of individual DAPs' involvements in HOT loci.

	- variant_density_values.txt
		enrichment values of various types of variants (GWAS, eQTLs, ClinVar, raQTLs, caQTLs) in HOT loci and other compared regions (DHS, enhancers, promoters).

	- windows_400_hg19.bed.gz
		file with all the tiled 400bp regions of hg19 genome used in the study.