KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
RNA-seq and genotyping array data (in this paper)	Marselli et al., 2020	EGA: EGAS00001005535
RNA-seq and genotyping array data	Fadista et al., 2014	GEO:GSE50244
RNA-seq and genotyping array data	van de Bunt et al., 2015	EGA:EGAD00001001601
RNA-seq data	Cnop et al., 2014	GEO:GSE53949
RNA-seq and genotyping array data	Akerman et al., 2017	EGA:EGAS00001002865
RNA-seq and genotyping array data	Miguel-Escalada et al., 2019; data not shown	EGA pending accession number
Expression array	Solimena et al., 2018	GEO:GSE76896
DNA-methylation	Hall et al., 2014	EGA:EGAD00001003946
Bisulphite sequencing	Thurner et al., 2018	EGA:EGAD00001003947
Cohesin	Miguel-Escalada et al., 2019	EGA:EGAD00001005203
Mediator	Miguel-Escalada et al., 2019	EGA:EGAD00001005203
H3K27ac	Miguel-Escalada et al., 2019	EGA:EGAD00001005203
ATAC-seq	Miguel-Escalada et al., 2019	EGA:EGAD00001005203
Islet regulome annotations, ChIP-seq and ATAC-seq processed files	Miguel-Escalada et al., 2019	EGA:EGAD00001005203
Pancreatic islet enhancer clusters	Pasquali et al., 2014
H3K4me1	Pasquali et al., 2014
Long non-coding RNAs (lncRNAs) annotation	Akerman et al., 2017
Pancreatic islet open chromatin DNase	Stitzel et al., 2010	ENCODE (2012–2016) Open Chromatine Dnase
Pancreatic islet open chromatin DNase	Gaulton et al., 2010	ENCODE (2012–2016) Open Chromatine Dnase
Glycemic traits data	MAGIC investigators (http://magicinvestigators.org.); members of MAGIC are provided in Appendix S1
70KforT2D GWAS meta-analysis summary statistics	Bonàs-Guarch et al., 2018	http://cg.bsc.es/70kfort2d/
DIAGRAM 1000G GWAS meta-analysis Stage 1 Summary statistics	Scott et al., 2017	https://diagram-consortium.org/downloads.html
DIAGRAM Trans-ethnic T2D GWAS meta-analysis	Mahajan et al., 2014	https://diagram-consortium.org/downloads.html
DIAMANTE T2D GWAS meta-analysis	Mahajan et al., 2018	https://diagram-consortium.org/downloads.html
GTEx Analysis V7 - Transcript TPMs	GTEx Portal	https://www.gtexportal.org/home/
FastDMA probe full annotation	Wu et al., 2013	http://bioinfo.au.tsinghua.edu.cn/member/jgu/fastdma/
Gene Ontology	The Gene Ontology Consortium, 2017	http://geneontology.org/
Reactome	Reactome Pathway database	https://reactome.org/download-data/
DisGeNET, May 2017	Piñero et al., 2016	https://www.disgenet.org/
GWAS Catalog version 1.0 release 2021-06-08	MacArthur et al., 2017	https://www.ebi.ac.uk/gwas/downloads
Ensembl Variant Effect Predictor version 87.27	McLaren et al., 2016	https://m.ensembl.org/info/data/ftp/index.html
RefSeq BUILD.37.3	O’Leary et al., 2016	ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/BUILD.37.3
Gencode v23 lift 37 annotation	Frankish et al., 2019	ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_23/GRCh37_mapping/gencode.v23lift37.annotation.gtf.gz
gnomAD version 2.0.2	gnomAD database	https://gnomad.broadinstitute.org/downloads