Reagent/Resource	Reference or source	Identifier or catalogue number
Software
GRaNIE R package	https://bioconductor.org/packages/GRaNIE/
GRaNPA R package	https://git.embl.de/grp‐zaugg/GRaNPA
Gephi 0.10.1	https://gephi.org/
DESeq2 R package	https://bioconductor.org/packages/DESeq2/
GeneOverlap R package	https://bioconductor.org/packages/GeneOverlap
fgsea R package	https://bioconductor.org/packages/fgsea
UCSC liftOver web interface	https://genome.ucsc.edu/cgi‐bin/hgLiftOver
External gene regulatory networks
Dorothea	Garcia‐Alonso et al (2019)
TRRUST	Han et al (2018)
ChEA3	Keenan et al (2019)
ANANSE	Xu et al (2021)
Other databases and resources
ReMap 2022	Hammal et al (2022)
FANTOM5 Human Enhancer Tracks	https://slidebase.binf.ku.dk/human_enhancers/presets Andersson et al (2014).	https://slidebase.binf.ku.dk/human_enhancers/presets/serve/macrophage
eQTL catalogue	https://www.ebi.ac.uk/eqtl/
LDSC Github repository	https://github.com/bulik/ldsc
General genomic features dataset	https://alkesgroup.broadinstitute.org/LDSCORE/
Fine‐mapped GWAS variants for autoimmune diseases	“PICS2‐GWAScat‐2020‐05‐22.txt.gz” from https://pics2.ucsf.edu