Key Resources Table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Experimental Models: Cell Lines
Human WTC	Miyaoka et al. 2014	https://doi.org/10.1038/nmeth.2840
Human HS1	Coriell Cell Repository	AG07095
Chimpanzee Pt2	Coriell Cell Repository	S003611
Chimpanzee Pt5	Coriell Cell Repository	PR00738
Antibodies
monoclonal mouse anti-Nestin	Abcam	Abcam AB6142
polyclonal rabbit anti-Pax6	Abcam	Abcam AB5790
polyclonal rabbit anti-GFAP	Chemicon	Chemicon AB5804
Recombinant DNA
pLS-mP	Nadav Ahituv	Addgene 81225
pLS-mP-Luc	Nadav Ahituv	Addgene106253
pLS-SV40-mP-Rluc	Nadav Ahituv	Addgene106292
Hsp68-LacZ vector	Nadav Ahituv	Addgene 37843
dCAS9-VP64_Blast	Feng Zhang	Addgene 61425
Oligonucleotides
Forward primer for Gapdh	This paper	GTCTCCTCTGACTTCAACAGCG
Reverse primer for Gapdh	This paper	ACCACCCTGTTGCTGTAGCCAA
Forward primer for Rock2	This paper	CGAGCCGCCAGAGAGAG
Reverse primer for Rock2	This paper	CCAAGGAAIIIAAGCCATCCAGC
Forward primer for E2f6	This paper	TACCCAGTCTCCTCCTGGAC
Reverse primer for E2f6	This paper	TATTTTTGATGGCAGCAGGC
Deposited Data
Raw and processed MPRA, ChlP-seq, ATAC-seq, and Hi-C sequencing data	This paper	GEO: GSE149268
Human Accelerated Regions	Hubisz and Pollard 2014	https://doi.org/10.1016/j.gde.2014.07.005
JASPAR 2020 transcription factor binding sites	Castro-Mondragon et al. 2022	https://jaspar.genereg.net
HOCOMOCO v11 transcription factor binding models	Kulakovskiy et al. 2018	https://hocomoco11.autosome.org
Raw and Processed ChlP-seq, ATAC-seq, and DNase-seq sequencing data	ENCODE Consortium	Table S3
Validated human enhancers	Visel et al. 2007	https://enhancer.lbl.gov
TF footprints in ENCODE tissues	Funk et al. 2020	https://data.nemoarchive.org/other/grant/sament/sament/footprint_atlas
Genomes for computing LD blocks by super-population	1000 Genomes Project Consortium	https://www.internationalgenome.org/data/
Multi-species alignment	Zoonomia Consortium	https://doi.org/10.1038/s41586-020-2876-6
Hi-C chromatin loops	Won et al. 2016	https://doi.org/10.1038/nature19847
PCHi-C chromatin loops	Song et al. 2019	https://doi.org/10.1038/s41588-019-0472-1
PLAC-seq chromatin loops	Song et al. 2020	https://doi.org/10.1038/s41586-020-2825-4
Software and Algorithms
pandas	McKinney 2012	https://pandas.pydata.org
scikit-learn	Pedregosa et al. 2011	https://scikit-learn.org
xgboost	Chen and Guestrin 2016	https://github.com/dmlc/xgboost
R	R Development Core Team 2018	https://www.r-project.org
bioconductor	Huber et al. 2015	https://www.bioconductor.org
limma	Ritchie et al. 2015	https://doi.org/10.18129/B9.bioc.limma
bedtools2	Quinlan and Hall 2010	https://github.com/arq5x/bedtools2
ENCODE ATAC-seq pipeline	Lee et al. 2016	https://github.com/ENCODE-DCC/atac-seq-pipeline
ENCODE ChlP-seq pipeline	Lee et al. 2016	https://github.com/ENCODE-DCC/chip-seq-pipeline2
HlNT	Gusmao et al. 2014	https://github.com/CostaLab/reg-gen
Sei	Chen et al. 2022	https://github.com/FunctionLab/sei-framework
distiller	Goloborodko et al. 2019	https://github.com/open2c/distiller-nf
juicer	Durand et al. 2016	https://github.com/aidenlab/juicer
mustache	Ardakany et al. 2020	https://github.com/ay-lab/mustache
plink	Purcell et al. 2007	https://www.cog-genomics.org/plink/1.9
UMAP	McInnes et al. 2018	https://github.com/lmcinnes/umap
jvarkit	Lindenbaum 2021	https://github.com/lindenb/jvarkit
mafslnRegion	Kent et al. 2002	https://hgdownload.soe.ucsc.edu/admin/exe
msa_view	Siepel et al. 2004	https://github.com/CshlSiepelLab/phast
kallisto	Bray et al. 2016	https://github.com/pachterlab/kallisto
g:Profiler	Raudvere et al. 2019	https://biit.cs.ut.ee/gprofiler/gost
Enhancer prediction	This paper	https://doi.org/10.5281/zenodo.7349179