REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Association results	This study	Table S2
Resource for Genetic Epidemiology Research on Aging (GERA) genotype data	Kvale et al.55	dbGaP accession number: phs000788.v1.p2
Children’s Oncology Group (COG)/St. Jude Children’s Research Hospital study genotype data	Qian et al.17	dbGaP accession number: phs000638.v1.p1, phs000637.v1.p1
Genes-environments and Admixture in Latino Asthmatics (GALA II) whole-genome sequencing and RNA sequencing data	Kachuri et al.41	dbGaP accession number: phs000920
Study of African Americans, Asthma, Genes, and Environments (SAGE) whole-genome sequencing and RNA sequencing data	Kachuri et al.41	dbGaP accession number: phs000921
1000 Genomes Project Phase 3 data	1000 Genomes Project Consortium56	https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502
Genome Aggregation Database (gnomAD) v3.1	Karczewski et al.57	https://gnomad.broadinstitute.org/downloads#v3
Hematopoiesis single-cell ATAC-sequencing data	Yu et al.,27 Granja et al.,58 Satpathy et al.59	https://github.com/GreenleafLab/MPAL-Single-Cell-2019, https://github.com/GreenleafLab/10x-scATAC-2019
Hematopoiesis single-cell RNA-sequencing data	Granja et al.58	https://github.com/GreenleafLab/MPAL-Single-Cell-2019
ATAC-sequencing data from 156 B cell ALL patients	Barnett et al.29	GEO: GSE226400
IKZF1 ChIP-seq data for GM12878	ENCODE Project Consortium60	GEO: GSE105587
Promoter capture Hi-C data for GM12878	Bhattacharyya et al.61	https://doi.org/10.5281/zenodo.3255048
eQTL summary statistics, ancestry-specific eQTLs, and TWAS models developed using data from GALA II and SAGE participants	Kachuri et al.41	https://doi.org/10.5281/zenodo.7735723
GTEx Consortium eQTL data	GTEx Consortium23	https://www.gtexportal.org/home/
eQTLGen Consortium eQTL data	Võsa et al.24	https://eqtlgen.org/cis-eqtls.html
ImmuNexUT eQTL data	Ota et al.25	https://www.immunexut.org/
Pre-calculated trees for each 1KG population	Speidel et al.62	https://zenodo.org/record/3234689#.Y2VdouzML0p/
Ancient genome shotgun sequencing data	Posth et al.,63 Mallick et al.,64 Moreno-Mayar et al.,65 Scheib et al.,66 Lindo et al.,67 de la Fuente et al.,68 Capodiferro et al.,69 Rasmussen et al.,70 Rasmussen et al.,71 Raghavan et al.,72 Skoglund et al.73	ENA: PRJEB28961, PRJEB9586, ERP010710, PRJEB29074, PRJEB25445, PRJNA470966, PRJEB24629, PRJEB42372, PRJEB9733 NCBI SRA: SRX381032, SRS937952
Human genome reference sequence hg38	UCSC Genome Browser	https://hgdownload.soe.ucsc.edu/downloads.html
Software and algorithms
PLINK v2.0	Chang et al.74	https://www.cog-genomics.org/plink/2.0/
LDLink	Machiela et al.75	https://ldlink.nih.gov/
TOPMed Imputation Server	Taliun et al.76	https://imputation.biodatacatalyst.nhlbi.nih.gov/
susieR	Zou et al.,77 Wang et al.78	https://github.com/stephenslab/susieR
RFMix	Maples et al.79	https://github.com/slowkoni/rfmix
ADMIXTURE	Alexander et al.80	https://dalexander.github.io/admixture/download.html
Relate	Speidel et al.62	https://myersgroup.github.io/relate/
samtools	Li et al.81	https://www.htslib.org/
SRA Toolkit	Github	https://github.com/ncbi/sra-tools
cutadapt	Martin82	https://cutadapt.readthedocs.io/en/stable/
FastQC	Github	https://github.com/s-andrews/FastQC
Bowtie2	Langmead et al.83	https://bowtie-bio.sourceforge.net/bowtie2
CHiCAGO	Cairns et al.84	https://www.bioconductor.org/packages/release/bioc/html/Chicago.html
LI-COR Image Studio Lite	LICOR Biosciences	RRID: SCR_013715
FlowJo	FlowJo LLC	RRID: SCR_008520
Chemicals, peptides, and recombinant proteins
Roche EDTA-free complete protease inhibitor cocktail	Roche	Cat: 11697498001
RIPA Buffer	Thermo Scientific	Cat: 89900
Dulbecco’s Modified Eagle Medium-High Glucose (DMEM)	Life Technologies	Cat: 11965-118
Iscove’s Modified Dulbecco’s Medium (IMDM)	StemCell Technologies	Cat: 36150
Fetal Bovine Serum (FBS)	BioTechne	Cat: S11550
Penicillin-Streptomycin	GIBCO	Cat: 15140-122
StemSpan SFEM II medium	StemCell Technologies	Cat: 02690
StemSpan CC100	StemCell Technologies	Cat: 02690
2-mercaptoethanol	Gibco	Cat: 21985023
PBS	GIBCO	Cat: 10010-023
L-Glutamine	Thermo Fisher Scientific	Cat: 25-030-081
Penicillin/Streptomycin	Life Technologies	Cat: 15140-122
Electroporation enhancer	IDT	Cat: 1075915
P3 Lonza buffer with supplement	Lonza	Cat: V4XP-3032
HiFi Cas9 Nuclease V3	IDT	Cat: 1081061
RPMI	Life Technologies	Cat: 11875085
EasySep Human CD34 Positive Selection Kit II	StemCell Technologies	Cat: 17856
RosetteSep Human Hematopoietic Progenitor Cell Enrichment Cocktail	StemCell Technologies	Cat: 15066
Ficoll-Paque	GE Healthcare	Cat: 45-001-751
TPO	Peprotech	Cat: 300-18
Recombinant IL7	StemCell Technologies	Cat: 78053
AllPrep DNA/RNA Mini kit	QIAGEN	Cat: 80204
OneShot TOP10 Chemically Competent Cells	Invitrogen	Cat: C404006
4–12% Criterion XT Bis-Tris Protein Gel	Bio-Rad	Cat: 3450124
Blocking buffer	LICOR Biosciences	Cat: 927-70001
7-AAD	BD Biosciences	Cat: 51-68981E
Recombinant Anti-Ikaros antibody	Abcam	Cat: ab191394; RRID: AB_3073859
Monoclonal Beta Actin Antibody	Santa Cruz Biotechnology	Cat: sc-47778; RRID: AB_626632
Platinum II Hot-Start PCR Master Mix	Invitrogen	Cat: 14000012
Tween 20	Sigma Aldrich	Cat: P9416
IRDye Secondary Antibodies	LI-COR Biosciences	Cat: 926–68072; RRID: AB_10953628Cat: 926-32212; RRID: AB_621847
FcR Blocking Reagent	Miltenyi	Cat: 130-059-901
CD34-Alexa488	BioLegend	Cat: 343517; RRID: AB_1937204
CD10-PE	Beckman-Coulter	Cat: IM1915U; RRID: AB_131294
CD19-BV421	BD Biosciences	Cat: 562440; RRID: AB_11153299
CD20-Pe-Cy7	BD Biosciences	Cat: 560735; RRID: AB_1727450
CD33-APC	BioLegend	Cat: 303407; RRID: AB_314351
Lenti-X Integration Site Analysis Kit	Takara	Cat: 631263
NucleoBond Xtra Maxi	Macherey-Nagel	Cat: 740424.50
Oligonucleotides
Primers and oligonucleotides	IDT	See STAR Methods
sgRNAs	Synthego	See STAR Methods
Recombinant DNA
pLKO lentiviral construct	Genetic Perturbation Platform, Broad Institute	Cat: TRC046
Biological samples
Human CD34+ hematopoietic stem and progenitor cells, adult	Fred Hutchinson Cancer Research Center	N/A
Cord Blood Unit for umbilical cord-derived CD34+ hematopoietic stem and progenitor cells	Dana Farber Pasquarello Tissue Bank	N/A
Experimental models: Cell lines
293T cells	ATCC	Cat: CRL-3216
Reh cells	ATCC	Cat: CRL-8286
MS-5	DSMZ-German Collection of Microorganisms and Cell Cultures	Cat: ACC 441
HepG2	ATCC	Cat: HB-8065