Table 4:

Epigenomic Resources for QTL mapping

Encyclopedia of DNA Elements (ENCODE)	Contains experimental information from ChIP-seq, ATAC-seq, Hi-C, and whole genome bisulfite sequencing data for human and mouse; data is integrated with USCS Genome Browser for visualization (62, 191)	https://www.encodeproject.org/
Functional Mapping and Annotation (FUMA) of GWAS	Standardized toolset to prioritize candidate genes from GWAS data inputs, using 18 data repositories and tools; output includes predicted SNP functions, chromatin states and 3D interactions (337)	https://fuma.ctglab.nl/
MRC-IEU EWAS (Epigenome-Wide Association Study) Catalog	Contains SNPs influencing epigenetic QTL extracted from EWAS literature, performed 41 EWAS on SNPs in the GEO database (14)	http://www.ewascatalog.org/
International Human Epigenome Consortium	Produces reference epigenome maps from curated datasets in >600 tissues. Contains contributions from ENCODE with a portal of several additional analysis tools to search by tissue source or assay type (30)	https://epigenomesportal.ca/ihec/
3DSNP Database	Database containing 3D and local chromatin interaction data from 3C-based high throughput methods. Useful for predictions on the effects of putative regulatory SNPs based on chromatin structural information (190)	http://cbportal.org/3dsnp/

Resources containing published human and animal epigenetic data, designed for use in QTL mapping, or in silico predictions of candidate genes