KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
PITX1 (G-4) X antibody	Santa Cruz Biotechnology, NJ, USA	sc-271435; RRID: AB_10658969
Bacterial and Virus Strains
E. coli DH10B	ThermoFisher Scientific	18297010
Biological Samples
Human E59 embryonic sample	University of Washington Birth Defects Research Laboratory	H27242
Human Knee MRI Image Data	OA Biomarkers Consortium Project for the National Institutes of Health (FNIH) Project	http://oai.epi-ucsf.org./datarelease/
Chemicals, Peptides, and Recombinant Proteins
Collagenase II	VWR	80056–222
Nextera Tn5 transposase	Illumina	#FC-121–1030
Critical Commercial Assays
SuperScript III First Strand cDNA Synthesis Reaction kit	Life Technologies	18090010
Pyrosequencing PSQ96 HS System	QIAGEN	PSQ H96A
Direct-zol RNA Miniprep kit	Zymo Research Corporation	R2072
Applied Biosystems Power SYBR master mix	Thermo Fisher Scientific	4368577
Lipofectamine 2000	Invitrogen	11668–019
Zymo-SpinTM ChIP Kit	Zymo Research Corporation	D5210
NEBNext High-Fidelity PCR Master Mix	NEB	M0541L
KAPA Library Quantification Complete Kit	KAPA	KK4824
Deposited Data
E15.5 Mouse Appendicular Skeleton ATAC-seq	This paper	GEO: GSE122877
E59 Human Appendicular Skeleton ATAC-seq	This paper	GEO: GSE122877
Mouse reference genome NCBI build GRCm38.p6	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26
Human reference genome NCBI build 37, GRCh37	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
BMDC ChIP-seq (H3K27ac)	Roadmap Epigenomics	GEO: GSE17312
Human E47 Limb Bud H3K27ac ChIP-seq	Cotney et al., 2013	GEO: GSM1039552 GSM1039553
GM12878 ATAC-seq	Buenrostro et al., 2013	GEO: GSE47753
Pitx1 ChIP-seq	Infante et al., 2013	GEO: GSE41591
ENCODE TF ChIP-seq	ENCODE Project Consortium, 2012	See Table S2, Sheets 4–6 for accession codes
Mouse CTCF ChIP-seq	DeMare et al., 2013	GEO: GSE42237
Mouse Sox9 ChIP-seq	Ohba et al., 2015	GEO: GSE69109
Mouse Runx2 ChIP-seq	Meyer et al., 2014	GEO: GSM1027496
Mouse RARb	He et al., 2013	GEO: GSE53736, GSM1299599
Mouse Shox2 ChIP-seq	Ye et al., 2016	GEO: GSM2177161
PhyloP20ways (hg38)	UCSC	http://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP20way/
PhyloP100ways (hg38)	UCSC	http://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/
Multiz20way Alignment	UCSC	http://hgdownload.cse.ucsc.edu/goldenpath/hg38/multiz20way/
1000 Genomes Phase 3 Data	1000 Genomes Project Consortium	ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Great Apes Diversity Project (GADP) Data	Prado-Martinez et al., 2013	https://eichlerlab.gs.washington.edu/greatape/data/
RepeatMasker (hg19)	UCSC Table Browser	https://genome.ucsc.edu/cgi-bin/hgTables
UK Biobanks Summary Statistics - Selfreported OA	http://www.nealelab.is/uk-biobank/	http://ldsc.broadinstitute.org/gwashare, http://www.nealelab.is/uk-biobank/
LDSC Baseline LD Model, 1KG3 reference allele frequencies, plink files and weights	Alkes Group	https://data.broadinstitute.org/alkesgroup/LDSCORE
Estonian Biocenter Human Genome Diversity Panel (EGDP)	Pagani et al., 2016	https://evolbio.ut.ee/CGgenomes_VCF/
Human-Chimp Whole-Genome Alignment (hg38 - panTro4)	UCSC	http://hgdownload.cse.ucsc.edu/goldenPath/hg38/vsPanTro4/
Experimental Models: Cell Lines
Human embryonic kidney (HEK293T)	ATCC	CRL-11268
Human T/C-28a2 chondrocytes	Mary Goldring	SCC042
Mouse NIH 3T3	ATCC	CRL-1658
Experimental Models: Organisms/Strains
R4 enhancer lacZ line	Harvard Genome Modification Facility	PHC21
R4+/− enhancer null mouse line	Harvard Genome Modification Facility	R4(R37)
R4rs6060369-T/+ single allelic replacement mouse line	Applied StemCell	MC140
C57BL/6J, wildtype	Jackson Laboratories	000664
129X1SVJ, wildtype	Jackson Laboratories	000691
FVB/NJ, wildtype	Jackson Laboratories	001800
Oligonucleotides
See Table S9 for generated primers used in study	This Paper	N/A
See Table S9 for generated sgRNAs used in study	This Paper	N/A
sg1:ACAGGGTGGGAGCGCTCAAT	Applied StemCell	N/A
sg2: GGGTGGGAGCGCTCAATAGG	Applied StemCell	N/A
Chr2-Reg-III-PM.F CAGGATTCGATG GCTGCTATTACTGAATG	Applied StemCell	N/A
Chr2-Reg-III-PM.R CACCTCAGCA GAGAGCG	Applied StemCell	N/A
Allele-specific Expression primers	EpigenDx	N/A
Recombinant DNA
PX458 plasmid	Addgene	101731
pGL4.23 Firefly luciferase	Promega	E8411
pGL4.74 Renilla luciferase	Promega	E6921
Software and Algorithms
Bowtie version 2.3.2	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Samtools version 1.5	Li, 2011a	http://samtools.sourceforge.net/
MACS2 version 2.1.1.2	Zhang et al., 2008	https://github.com/taoliu/MACS
Irreproducible Discovery Rate	Li et al., 2011	https://www.encodeproject.org/software/idr/, https://codeload.github.com/nboley/idr/tar.gz/2.0.0
Bedtools version 2.26.0	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest/
HOMER version 4.10	Heinz et al., 2010	http://homer.ucsd.edu/homer/
R base version 3.4.4	R Development Core Team, 2008	https://www.r-project.org/
regioneR version 1.8.1	Gel et al., 2016	http://bioconductor.org/packages/release/bioc/html/regioneR.html
GREAT version 3.0.0	McLean et al., 2010	http://great.stanford.edu/public/html/
car version 3.0.3	Fox and Weisberg, 2019	https://cran.r-project.org/web/packages/car/index.html
fitdistrplus version 1.0–14	Delignette-Muller and Dutang, 2015	https://cran.r-project.org/web/packages/fitdistrplus/index.html
Tabix version 1.7.24	Li, 2011a	http://www.htslib.org/doc/tabix.html
bcftools version 1.8	Li, 2011a	https://samtools.github.io/bcftools/bcftools.html
vcftools 0.1.15	Danecek et al., 2011	https://vcftools.github.io/
ProxyFinder	Raychaudhuri Lab	https://github.com/immunogenomics/harmjan/tree/master/ProxyFinder
LDSC	Finucane et al., 2015	https://github.com/bulik/ldsc
Pegas version 0.11	Paradis, 2010	https://cran.r-project.org/web/packages/pegas/index.html
ComplexHeatmap version 1.17.1	Gu et al., 2016	https://github.com/jokergoo/ComplexHeatmap
Factoextra version 1.0.5	Kassambara and Mundt, 2017	https://cran.r-project.org/web/packages/factoextra/index.html
Cluster version 2.0.7–1	Maechler et al., 2018	https://cran.r-project.org/web/packages/cluster/index.html
Plink version 1.90	Chang et al., 2015	www.cog-genomics.org/plink/1.9/
Haploview version 4.2	Barrett et al., 2005	https://www.broadinstitute.org/haploview/haploview
RaxML version 7.3.0	Stamatakis, 2006	https://github.com/stamatak/standard-RAxML
motifbreakR version 1.6.0	Coetzee et al., 2015	https://bioconductor.org/packages/release/bioc/html/motifbreakR.html
MotifDb version 1.6.0	Shannon and Richards, 2014	http://bioconductor.org/packages/release/bioc/html/MotifDb.html
Haploreg version 4.162	Ward and Kellis, 2012	https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php
Uniprobe	Hume et al., 2015	http://the_brain.bwh.harvard.edu/uniprobe/about.php/
Crossmap version 0.3.3	Zhao et al., 2014	http://crossmap.sourceforge.net/
BEAGLE5	Browning et al., 2018	https://faculty.washington.edu/browning/beagle/beagle.html
Other
Allele-specific Expression Assays	EpigenDx	N/A
MicroCT imaging	Center for Skeletal Research, MGH	N/A
Primer oligonucleotide synthesis	Integrated DNA Technologies, Inc	N/A
Human oligonucleotide synthesis	TwistBioscience	N/A
ATAC-sequencing	Harvard Bauer Core Facility	N/A
CRISPR Mi-seq sequencing	MGH CCIB DNA Core	N/A
Mouse R4 element targeting	Applied StemCell & Harvard Genome Modification Facility	N/A