mm10_v2_chr9_-_53975246_53975348	6.2276	Msx3	ENSMUST00000048409.7|Elmod1|ENSMUSG00000041986.9|ELMO/CED-12 domain containing 1
mm10_v2_chrX_-_143933204_143933311	4.17394	Msx3	ENSMUST00000112851.1|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000112856.2|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000033642.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chrX_-_143933089_143933142	3.72083	Msx3	ENSMUST00000087313.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chr2_-_45117349_45117395	3.50972	Msx3	ENSMUST00000176438.2|Zeb2|ENSMUSG00000026872.10|zinc finger E-box binding homeobox 2
mm10_v2_chr1_-_158356258_158356313	3.09766	Msx3	ENSMUST00000004133.8|Brinp2|ENSMUSG00000004031.8|bone morphogenic protein/retinoic acid inducible neural-specific 2
mm10_v2_chr5_+_14514918_14514951	2.83753	Msx3	ENSMUST00000030691.10|Pclo|ENSMUSG00000061601.9|piccolo (presynaptic cytomatrix protein) 	ENSMUST00000182407.1|Pclo|ENSMUSG00000061601.9|piccolo (presynaptic cytomatrix protein)
mm10_v2_chr4_-_14621805_14621819	2.57806	Msx3	ENSMUST00000042221.7|Slc26a7|ENSMUSG00000040569.7|solute carrier family 26, member 7
mm10_v2_chr10_+_81257277_81257309	2.50826	Msx3	ENSMUST00000117488.1|Matk|ENSMUSG00000004933.11|megakaryocyte-associated tyrosine kinase 	ENSMUST00000105328.3|Matk|ENSMUSG00000004933.11|megakaryocyte-associated tyrosine kinase 	ENSMUST00000121205.1|Matk|ENSMUSG00000004933.11|megakaryocyte-associated tyrosine kinase
mm10_v2_chr15_+_82252397_82252475	2.47395	Msx3	ENSMUST00000136948.1|1500009C09Rik|ENSMUSG00000068099.4|RIKEN cDNA 1500009C09 gene
mm10_v2_chr13_+_83732438_83732566	2.37672	Msx3	ENSMUST00000182701.1|C130071C03Rik|ENSMUSG00000050334.6|RIKEN cDNA C130071C03 gene
mm10_v2_chr2_+_125136692_125136769	2.37149	Msx3	ENSMUST00000099452.2|Ctxn2|ENSMUSG00000074872.2|cortexin 2
mm10_v2_chr10_+_39612934_39612934	2.3588	Msx3	ENSMUST00000019987.6|Traf3ip2|ENSMUSG00000019842.6|TRAF3 interacting protein 2
mm10_v2_chr5_+_88583527_88583590	2.25505	Msx3	ENSMUST00000031229.6|Rufy3|ENSMUSG00000029291.7|RUN and FYVE domain containing 3
mm10_v2_chr15_+_44787746_44787782	2.1967	Msx3	ENSMUST00000181839.1|2310069G16Rik|ENSMUSG00000097102.1|RIKEN cDNA 2310069G16 gene
mm10_v2_chr1_-_52190901_52190915	2.08327	Msx3	ENSMUST00000156887.1|Gls|ENSMUSG00000026103.8|glutaminase 	ENSMUST00000129107.1|Gls|ENSMUSG00000026103.8|glutaminase
mm10_v2_chr2_-_33087169_33087253	1.97374	Msx3	ENSMUST00000102810.3|Garnl3|ENSMUSG00000038860.9|GTPase activating RANGAP domain-like 3
mm10_v2_chr18_+_37819543_37819570	1.87882	Msx3	ENSMUST00000055935.5|Pcdhga9|ENSMUSG00000023036.8|protocadherin gamma subfamily A, 9
mm10_v2_chr9_-_15301555_15301607	1.86502	Msx3	ENSMUST00000034414.8|4931406C07Rik|ENSMUSG00000031938.8|RIKEN cDNA 4931406C07 gene
mm10_v2_chr7_-_127895578_127895647	1.85308	Msx3	ENSMUST00000033074.6|Vkorc1|ENSMUSG00000096145.1|vitamin K epoxide reductase complex, subunit 1
mm10_v2_chr11_+_70018421_70018484	1.78474	Msx3	ENSMUST00000108588.1|Dlg4|ENSMUSG00000020886.10|discs, large homolog 4 (Drosophila)
mm10_v2_chr2_-_33086366_33086447	1.76718	Msx3	ENSMUST00000049618.2|Garnl3|ENSMUSG00000038860.9|GTPase activating RANGAP domain-like 3
mm10_v2_chr4_+_102254739_102254761	1.69317	Msx3	ENSMUST00000106907.2|Pde4b|ENSMUSG00000028525.10|phosphodiesterase 4B, cAMP specific
mm10_v2_chr16_+_11406618_11406675	1.67973	Msx3	ENSMUST00000122168.1|Snx29|ENSMUSG00000071669.8|sorting nexin 29
mm10_v2_chr10_+_88379217_88379299	1.50505	Msx3	ENSMUST00000130301.1|Gnptab|ENSMUSG00000035311.10|N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits 	ENSMUST00000020251.8|Gnptab|ENSMUSG00000035311.10|N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits
mm10_v2_chr17_+_21383725_21383766	1.44926	Msx3	ENSMUST00000056107.4|Zfp677|ENSMUSG00000062743.3|zinc finger protein 677 	ENSMUST00000162659.1|Zfp677|ENSMUSG00000062743.3|zinc finger protein 677
mm10_v2_chr6_+_134640940_134641097	1.44243	Msx3	ENSMUST00000062755.8|Loh12cr1|ENSMUSG00000042992.9|loss of heterozygosity, 12, chromosomal region 1 homolog (human)
mm10_v2_chr4_-_14621494_14621506	1.42508	Msx3	ENSMUST00000149633.1|Slc26a7|ENSMUSG00000040569.7|solute carrier family 26, member 7
mm10_v2_chr7_+_3645267_3645352	1.4068	Msx3	ENSMUST00000038913.9|Cnot3|ENSMUSG00000035632.10|CCR4-NOT transcription complex, subunit 3
mm10_v2_chr3_-_116253467_116253484	1.29303	Msx3	ENSMUST00000090473.5|Gpr88|ENSMUSG00000068696.5|G-protein coupled receptor 88
mm10_v2_chr12_+_72441852_72441866	1.22668	Msx3	ENSMUST00000162159.1|Lrrc9|ENSMUSG00000021090.9|leucine rich repeat containing 9
mm10_v2_chr9_+_44398176_44398176	1.05973	Msx3	ENSMUST00000165839.1|Slc37a4|ENSMUSG00000032114.8|solute carrier family 37 (glucose-6-phosphate transporter), member 4
mm10_v2_chr3_+_94837533_94837567	1.05451	Msx3	ENSMUST00000107270.2|Pogz|ENSMUSG00000038902.8|pogo transposable element with ZNF domain
mm10_v2_chr10_+_88379127_88379169	0.997319	Msx3	ENSMUST00000127615.1|Gnptab|ENSMUSG00000035311.10|N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits
mm10_v2_chr8_+_72219726_72219785	0.992339	Msx3	ENSMUST00000003123.8|Fam32a|ENSMUSG00000003039.8|family with sequence similarity 32, member A
mm10_v2_chr8_+_107031218_107031229	0.933132	Msx3	ENSMUST00000034388.9|Vps4a|ENSMUSG00000031913.9|vacuolar protein sorting 4a (yeast)
mm10_v2_chr12_+_72441933_72441970	0.914153	Msx3	ENSMUST00000161284.1|Lrrc9|ENSMUSG00000021090.9|leucine rich repeat containing 9
mm10_v2_chr7_+_103550368_103550368	0.879655	Msx3	ENSMUST00000106888.1|Olfr613|ENSMUSG00000078624.2|olfactory receptor 613
mm10_v2_chr4_-_129378116_129378116	0.839253	Msx3	ENSMUST00000030610.2|Zbtb8a|ENSMUSG00000028807.2|zinc finger and BTB domain containing 8a
mm10_v2_chr7_-_99141068_99141149	0.815029	Msx3	ENSMUST00000037968.8|Uvrag|ENSMUSG00000035354.8|UV radiation resistance associated gene
mm10_v2_chr4_-_14621669_14621786	0.811615	Msx3	ENSMUST00000143105.1|Slc26a7|ENSMUSG00000040569.7|solute carrier family 26, member 7
mm10_v2_chrX_-_75578188_75578247	0.810947	Msx3	ENSMUST00000033545.5|Rab39b|ENSMUSG00000031202.5|RAB39B, member RAS oncogene family
mm10_v2_chr13_+_67863324_67863328	0.753478	Msx3	ENSMUST00000078471.5|BC048507|ENSMUSG00000064063.5|cDNA sequence BC048507
mm10_v2_chr11_+_116843278_116843278	0.73713	Msx3	ENSMUST00000106370.3|Mettl23|ENSMUSG00000090266.4|methyltransferase like 23
mm10_v2_chrM_+_9870_9885	0.731046	Msx3	ENSMUST00000084013.1|mt-Nd4l|ENSMUSG00000065947.3|mitochondrially encoded NADH dehydrogenase 4L
mm10_v2_chr2_+_121956411_121956480	0.662158	Msx3	ENSMUST00000110578.1|Ctdspl2|ENSMUSG00000033411.10|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2
mm10_v2_chr18_+_57468478_57468541	0.620463	Msx3	ENSMUST00000091892.2|Ctxn3|ENSMUSG00000069372.2|cortexin 3
mm10_v2_chr10_-_85127977_85128035	0.589447	Msx3	ENSMUST00000050813.2|Mterfd3|ENSMUSG00000049038.2|MTERF domain containing 3
mm10_v2_chr11_+_53433299_53433357	0.5451	Msx3	ENSMUST00000018382.6|Gdf9|ENSMUSG00000018238.6|growth differentiation factor 9
mm10_v2_chr17_-_24527830_24527884	0.529548	Msx3	ENSMUST00000176353.1|Traf7|ENSMUSG00000052752.9|TNF receptor-associated factor 7 	ENSMUST00000176237.1|Traf7|ENSMUSG00000052752.9|TNF receptor-associated factor 7
mm10_v2_chr2_+_121956651_121956664	0.525875	Msx3	ENSMUST00000110574.1|Ctdspl2|ENSMUSG00000033411.10|CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2
mm10_v2_chr16_-_75766758_75766821	0.513946	Msx3	ENSMUST00000114244.1|Hspa13|ENSMUSG00000032932.8|heat shock protein 70 family, member 13 	ENSMUST00000046283.8|Hspa13|ENSMUSG00000032932.8|heat shock protein 70 family, member 13
mm10_v2_chr17_-_24527925_24527938	0.497132	Msx3	ENSMUST00000176652.1|Traf7|ENSMUSG00000052752.9|TNF receptor-associated factor 7
mm10_v2_chr3_+_94837702_94837723	0.461057	Msx3	ENSMUST00000107266.1|Pogz|ENSMUSG00000038902.8|pogo transposable element with ZNF domain 	ENSMUST00000042402.5|Pogz|ENSMUSG00000038902.8|pogo transposable element with ZNF domain 	ENSMUST00000107269.1|Pogz|ENSMUSG00000038902.8|pogo transposable element with ZNF domain
mm10_v2_chr15_+_38661904_38661981	0.432871	Msx3	ENSMUST00000022904.6|Atp6v1c1|ENSMUSG00000022295.7|ATPase, H+ transporting, lysosomal V1 subunit C1
mm10_v2_chr12_+_102128718_102128739	0.318488	Msx3	ENSMUST00000159329.1|Slc24a4|ENSMUSG00000041771.7|solute carrier family 24 (sodium/potassium/calcium exchanger), member 4
mm10_v2_chr12_+_71136848_71136848	0.28525	Msx3	ENSMUST00000149564.1|2700049A03Rik|ENSMUSG00000034601.10|RIKEN cDNA 2700049A03 gene 	ENSMUST00000045907.8|2700049A03Rik|ENSMUSG00000034601.10|RIKEN cDNA 2700049A03 gene
mm10_v2_chr8_+_69659263_69659263	0.263212	Msx3	ENSMUST00000169125.1|Zfp964|ENSMUSG00000091764.1|zinc finger protein 964
mm10_v2_chr6_+_145934113_145934136	0.196347	Msx3	ENSMUST00000032383.7|Sspn|ENSMUSG00000030255.7|sarcospan
mm10_v2_chr3_-_41742471_41742548	0.177751	Msx3	ENSMUST00000026866.8|Sclt1|ENSMUSG00000059834.6|sodium channel and clathrin linker 1
mm10_v2_chr4_+_94739276_94739300	0.161157	Msx3	ENSMUST00000073939.6|Tek|ENSMUSG00000006386.9|endothelial-specific receptor tyrosine kinase 	ENSMUST00000102798.1|Tek|ENSMUSG00000006386.9|endothelial-specific receptor tyrosine kinase
mm10_v2_chrX_+_101449078_101449089	0.0997073	Msx3	ENSMUST00000033674.5|Itgb1bp2|ENSMUSG00000031312.5|integrin beta 1 binding protein 2
mm10_v2_chr7_+_101896817_101896961	0.07492	Msx3	ENSMUST00000143835.1|Anapc15|ENSMUSG00000030649.11|anaphase prompoting complex C subunit 15
mm10_v2_chr12_-_71136611_71136701	0.0375885	Msx3	ENSMUST00000021486.8|Timm9|ENSMUSG00000021079.9|translocase of inner mitochondrial membrane 9 	ENSMUST00000166120.1|Timm9|ENSMUSG00000021079.9|translocase of inner mitochondrial membrane 9
mm10_v2_chr2_-_20943413_20943424	0.0302871	Msx3	ENSMUST00000140230.1|Arhgap21|ENSMUSG00000036591.9|Rho GTPase activating protein 21
mm10_v2_chr2_-_160619971_160619971	0.00158062	Msx3	ENSMUST00000109473.1|Gm14221|ENSMUSG00000078956.2|predicted gene 14221
