REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Human epigenome	ENCODE project13	Table S1
Human gene expression	ENCODE project13	Table S1
Human chromatin state	Pan et al.18	Table S2
Pig epigenome	Pan et al.18; Zhao et al.19	Table S3
Pig gene expression	Pan et al.18; Zhao et al.19	Table S6
Pig chromatin state	Pan et al.18	Table S4
Orthologous SNPs between human and pig	1,000 Genome Project30	http://ftp.1000genomes.ebi.ac.uk
Human GWAS summary statistics	UK Biobank	http://www.ukbiobank.ac.uk
Software and algorithms
R 4.1	R Core Team	https://www.r-project.org/
Python version 3.6.9	Van Rossum	https://www.python.org/
DeepGCF	This paper	https://github.com/liangend/DeepGCF and https://doi.org/10.5281/zenodo.8087963
LDSC version 1.0.1	Finucane et al.41	https://github.com/bulik/ldsc
Polyfun	Weissbrod et al.42	https://github.com/omerwe/polyfun
SBayesRC	Zheng et al.43	https://github.com/zhilizheng/SBayesRC
R package MashR version 0.2.57	Urbut et al.36	https://github.com/stephenslab/mashr
SuSiE	Wang et al.44	https://stephenslab.github.io/susieR/index.html
LiftOver	Lee et al.46	https://genome.ucsc.edu/cgi-bin/hgLiftOver
Python package selene-sdk	Chen et al.47	https://github.com/FunctionLab/selene
Python package torch version 1.10.0	Paszke et al.48	https://pypi.org/project/torch/
Python package sklearn version 0.24.2	Pedregosa et al.49	https://scikit-learn.org/stable/
R package GREAT version 1.26.0	McLean et al.50	https://www.bioconductor.org/packages/release/bioc/html/rGREAT.html
BEDtools version 2.29.1	Quinlan and Hall51	http://bedtools.readthedocs.io/