August 12, 2020 Dataset Open Access

GREEN-DB: Genomic Regulatory Elements ENcyclopedia

Edoardo Giacopuzzi; Niko Popitsch; Jenny C Taylor

GREEN-DB is a standardized collection of 2.4 million regulatory elements in the human genome. Information on controlled gene(s), tissue(s) and associated phenotype(s) are provided for each element when possible. We also calculated a variation constraint metric (range 0-1) for these regulatory regions and showed that genes controlled by constrained regions are enriched for disease-associated genes and essential genes from mouse knock-out screenings.

The database also includes information from ENCODE TFBS and DNase peaks; ultra-conserved non-coding elements (UCNE), and super-enhancers (dbSuper).

This release includes 2 files:

• RegulatoryRegions.db.gz: The full database is available in SQLite format
• GREEN-DB_v2_bedfiles.tar.gz: Contains 2 BED files describing the regulatory regions and assciated information useful for variant annotations (controlled genes, closest gene, constraint metric).

To annotate a VCF file with information from GREEN-DB you can use our tools GREEN-VARAN (https://github.com/edg1983/GREEN-VARAN).

For more information on the GREEN-DB please refer to our publication (https://doi.org/10.1101/2020.09.17.301960) and to online documentation (https://green-varan.readthedocs.io/en/latest/)

GREEN-DB is free to use for academic users, please refer to the attached LICENSE file.