mm10_v2_chr1_-_190170671_190170744	11.9811	Msx2_Hoxd4	ENSMUST00000175916.1|Prox1|ENSMUSG00000010175.7|prospero-related homeobox 1
mm10_v2_chr5_-_62766153_62766246	11.7095	Msx2_Hoxd4	ENSMUST00000076623.4|Arap2|ENSMUSG00000037999.9|ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2
mm10_v2_chr1_-_190170178_190170237	9.84409	Msx2_Hoxd4	ENSMUST00000177288.1|Prox1|ENSMUSG00000010175.7|prospero-related homeobox 1
mm10_v2_chr6_-_36811361_36811361	8.75229	Msx2_Hoxd4	ENSMUST00000101534.1|Ptn|ENSMUSG00000029838.8|pleiotrophin
mm10_v2_chr3_+_62419668_62419668	6.69996	Msx2_Hoxd4	ENSMUST00000161057.1|Arhgef26|ENSMUSG00000036885.8|Rho guanine nucleotide exchange factor (GEF) 26
mm10_v2_chr2_-_63184253_63184292	6.56508	Msx2_Hoxd4	ENSMUST00000075052.3|Kcnh7|ENSMUSG00000059742.4|potassium voltage-gated channel, subfamily H (eag-related), member 7 	ENSMUST00000112454.1|Kcnh7|ENSMUSG00000059742.4|potassium voltage-gated channel, subfamily H (eag-related), member 7
mm10_v2_chr3_-_49757257_49757316	6.50307	Msx2_Hoxd4	ENSMUST00000035931.7|Pcdh18|ENSMUSG00000037892.8|protocadherin 18
mm10_v2_chr3_-_85741389_85741389	5.67523	Msx2_Hoxd4	ENSMUST00000094148.4|Fam160a1|ENSMUSG00000051000.11|family with sequence similarity 160, member A1
mm10_v2_chr2_+_4017727_4017745	5.56157	Msx2_Hoxd4	ENSMUST00000177457.1|Frmd4a|ENSMUSG00000026657.10|FERM domain containing 4A
mm10_v2_chr1_-_163725123_163725232	5.2203	Msx2_Hoxd4	ENSMUST00000159679.1|Mettl11b|ENSMUSG00000040113.8|methyltransferase like 11B
mm10_v2_chr2_-_63184170_63184195	4.4851	Msx2_Hoxd4	ENSMUST00000112452.1|Kcnh7|ENSMUSG00000059742.4|potassium voltage-gated channel, subfamily H (eag-related), member 7
mm10_v2_chr14_-_88471396_88471396	4.2487	Msx2_Hoxd4	ENSMUST00000061628.5|Pcdh20|ENSMUSG00000050505.6|protocadherin 20
mm10_v2_chr1_+_165788681_165788728	3.57219	Msx2_Hoxd4	ENSMUST00000161971.1|Cd247|ENSMUSG00000005763.9|CD247 antigen 	ENSMUST00000178336.1|Cd247|ENSMUSG00000005763.9|CD247 antigen 	ENSMUST00000005907.5|Cd247|ENSMUSG00000005763.9|CD247 antigen 	ENSMUST00000027849.4|Cd247|ENSMUSG00000005763.9|CD247 antigen
mm10_v2_chr9_+_22454290_22454290	3.00845	Msx2_Hoxd4	ENSMUST00000168332.1|Gm17545|ENSMUSG00000091159.1|predicted gene, 17545
mm10_v2_chr3_+_68869563_68869589	2.95818	Msx2_Hoxd4	ENSMUST00000054551.2|1110032F04Rik|ENSMUSG00000046999.2|RIKEN cDNA 1110032F04 gene
mm10_v2_chr5_-_62765618_62765656	2.91738	Msx2_Hoxd4	ENSMUST00000159470.1|Arap2|ENSMUSG00000037999.9|ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2
mm10_v2_chr1_+_165788746_165788769	2.72621	Msx2_Hoxd4	ENSMUST00000161559.2|Cd247|ENSMUSG00000005763.9|CD247 antigen
mm10_v2_chr15_-_79285502_79285537	2.58795	Msx2_Hoxd4	ENSMUST00000165408.1|Baiap2l2|ENSMUSG00000018126.9|BAI1-associated protein 2-like 2
mm10_v2_chr1_-_163289214_163289235	2.51482	Msx2_Hoxd4	ENSMUST00000183691.1|Prrx1|ENSMUSG00000026586.10|paired related homeobox 1
mm10_v2_chr3_-_66296807_66296837	2.25779	Msx2_Hoxd4	ENSMUST00000029419.7|Veph1|ENSMUSG00000027831.9|ventricular zone expressed PH domain-containing 1
mm10_v2_chr18_+_52767994_52768149	2.2022	Msx2_Hoxd4	ENSMUST00000025413.7|Sncaip|ENSMUSG00000024534.9|synuclein, alpha interacting protein (synphilin) 	ENSMUST00000163742.2|Sncaip|ENSMUSG00000024534.9|synuclein, alpha interacting protein (synphilin) 	ENSMUST00000178011.1|Sncaip|ENSMUSG00000024534.9|synuclein, alpha interacting protein (synphilin)
mm10_v2_chr9_-_114390633_114390687	2.15176	Msx2_Hoxd4	ENSMUST00000084881.4|Crtap|ENSMUSG00000032431.6|cartilage associated protein
mm10_v2_chr16_-_44016387_44016436	2.09094	Msx2_Hoxd4	ENSMUST00000036174.3|Gramd1c|ENSMUSG00000036292.7|GRAM domain containing 1C
mm10_v2_chr4_+_136143497_136143497	2.02526	Msx2_Hoxd4	ENSMUST00000008016.2|Id3|ENSMUSG00000007872.3|inhibitor of DNA binding 3
mm10_v2_chr3_+_138065052_138065078	1.94098	Msx2_Hoxd4	ENSMUST00000163080.2|1110002E22Rik|ENSMUSG00000090066.2|RIKEN cDNA 1110002E22 gene
mm10_v2_chr7_+_96522342_96522398	1.80603	Msx2_Hoxd4	ENSMUST00000129737.1|Tenm4|ENSMUSG00000048078.10|teneurin transmembrane protein 4
mm10_v2_chr12_+_36314160_36314171	1.80447	Msx2_Hoxd4	ENSMUST00000041407.5|Sostdc1|ENSMUSG00000036169.5|sclerostin domain containing 1
mm10_v2_chr2_-_33086366_33086447	1.7299	Msx2_Hoxd4	ENSMUST00000049618.2|Garnl3|ENSMUSG00000038860.9|GTPase activating RANGAP domain-like 3
mm10_v2_chrX_+_101640056_101640108	1.72005	Msx2_Hoxd4	ENSMUST00000119299.1|Ogt|ENSMUSG00000034160.7|O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase) 	ENSMUST00000044475.4|Ogt|ENSMUSG00000034160.7|O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)
mm10_v2_chr3_+_52268337_52268388	1.66697	Msx2_Hoxd4	ENSMUST00000053764.5|Foxo1|ENSMUSG00000044167.5|forkhead box O1
mm10_v2_chrX_+_56454871_56454887	1.63785	Msx2_Hoxd4	ENSMUST00000039374.2|Ddx26b|ENSMUSG00000035967.9|DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26B 	ENSMUST00000101553.2|Ddx26b|ENSMUSG00000035967.9|DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26B
mm10_v2_chr15_-_37459327_37459380	1.61431	Msx2_Hoxd4	ENSMUST00000119730.1|Ncald|ENSMUSG00000051359.8|neurocalcin delta 	ENSMUST00000120746.1|Ncald|ENSMUSG00000051359.8|neurocalcin delta
mm10_v2_chrX_+_150547375_150547459	1.56768	Msx2_Hoxd4	ENSMUST00000066337.6|Alas2|ENSMUSG00000025270.7|aminolevulinic acid synthase 2, erythroid 	ENSMUST00000112715.1|Alas2|ENSMUSG00000025270.7|aminolevulinic acid synthase 2, erythroid
mm10_v2_chr4_+_124657646_124657656	1.50545	Msx2_Hoxd4	ENSMUST00000053491.7|Pou3f1|ENSMUSG00000090125.2|POU domain, class 3, transcription factor 1
mm10_v2_chr19_+_26749726_26749877	1.49898	Msx2_Hoxd4	ENSMUST00000175842.1|Smarca2|ENSMUSG00000024921.10|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
mm10_v2_chr2_-_144527341_144527424	1.49742	Msx2_Hoxd4	ENSMUST00000163701.1|Dzank1|ENSMUSG00000037259.9|double zinc ribbon and ankyrin repeat domains 1 	ENSMUST00000081982.5|Dzank1|ENSMUSG00000037259.9|double zinc ribbon and ankyrin repeat domains 1
mm10_v2_chr13_+_75967704_75967753	1.41769	Msx2_Hoxd4	ENSMUST00000022081.1|Spata9|ENSMUSG00000021590.6|spermatogenesis associated 9
mm10_v2_chr17_-_25785324_25785343	1.38805	Msx2_Hoxd4	ENSMUST00000150324.1|Haghl|ENSMUSG00000061046.3|hydroxyacylglutathione hydrolase-like
mm10_v2_chr1_-_72284248_72284314	1.37529	Msx2_Hoxd4	ENSMUST00000097698.4|Pecr|ENSMUSG00000026189.7|peroxisomal trans-2-enoyl-CoA reductase 	ENSMUST00000027381.6|Pecr|ENSMUSG00000026189.7|peroxisomal trans-2-enoyl-CoA reductase
mm10_v2_chr1_+_159737510_159737510	1.35952	Msx2_Hoxd4	ENSMUST00000111669.3|Tnr|ENSMUSG00000015829.8|tenascin R
mm10_v2_chr8_-_120228221_120228297	1.30583	Msx2_Hoxd4	ENSMUST00000183235.1|A330074K22Rik|ENSMUSG00000097960.1|RIKEN cDNA A330074K22 gene
mm10_v2_chr5_-_107875035_107875107	1.29739	Msx2_Hoxd4	ENSMUST00000138111.1|Evi5|ENSMUSG00000011831.10|ecotropic viral integration site 5 	ENSMUST00000112642.1|Evi5|ENSMUSG00000011831.10|ecotropic viral integration site 5
mm10_v2_chrX_+_159708593_159708612	1.25735	Msx2_Hoxd4	ENSMUST00000080394.6|Sh3kbp1|ENSMUSG00000040990.11|SH3-domain kinase binding protein 1
mm10_v2_chr3_-_146495115_146495139	1.20628	Msx2_Hoxd4	ENSMUST00000093951.2|Spata1|ENSMUSG00000028188.7|spermatogenesis associated 1
mm10_v2_chr1_-_152625212_152625220	1.11016	Msx2_Hoxd4	ENSMUST00000027760.7|Rgl1|ENSMUSG00000026482.7|ral guanine nucleotide dissociation stimulator,-like 1
mm10_v2_chr1_-_133921393_133921414	1.04715	Msx2_Hoxd4	ENSMUST00000048432.5|Prelp|ENSMUSG00000041577.5|proline arginine-rich end leucine-rich repeat
mm10_v2_chr7_-_73541738_73541758	1.03436	Msx2_Hoxd4	ENSMUST00000169922.2|Chd2|ENSMUSG00000078671.4|chromodomain helicase DNA binding protein 2
mm10_v2_chr7_-_73537621_73537766	1.02641	Msx2_Hoxd4	ENSMUST00000172704.1|Chd2|ENSMUSG00000078671.4|chromodomain helicase DNA binding protein 2
mm10_v2_chr11_+_103133303_103133332	1.00191	Msx2_Hoxd4	ENSMUST00000107037.1|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2
mm10_v2_chr18_-_37969742_37969782	0.992364	Msx2_Hoxd4	ENSMUST00000166148.1|Fchsd1|ENSMUSG00000038524.7|FCH and double SH3 domains 1 	ENSMUST00000163131.1|Fchsd1|ENSMUSG00000038524.7|FCH and double SH3 domains 1 	ENSMUST00000043437.7|Fchsd1|ENSMUSG00000038524.7|FCH and double SH3 domains 1
mm10_v2_chr5_-_146220901_146220987	0.966825	Msx2_Hoxd4	ENSMUST00000169407.2|Rnf6|ENSMUSG00000029634.9|ring finger protein (C3H2C3 type) 6 	ENSMUST00000161331.1|Rnf6|ENSMUSG00000029634.9|ring finger protein (C3H2C3 type) 6 	ENSMUST00000159074.2|Rnf6|ENSMUSG00000029634.9|ring finger protein (C3H2C3 type) 6 	ENSMUST00000067837.3|Rnf6|ENSMUSG00000029634.9|ring finger protein (C3H2C3 type) 6
mm10_v2_chr4_-_40722307_40722398	0.959506	Msx2_Hoxd4	ENSMUST00000181475.1|Gm6297|ENSMUSG00000097123.1|predicted gene 6297
mm10_v2_chr4_-_129121889_129122063	0.945411	Msx2_Hoxd4	ENSMUST00000139450.1|Hpca|ENSMUSG00000028785.6|hippocalcin 	ENSMUST00000125931.1|Hpca|ENSMUSG00000028785.6|hippocalcin 	ENSMUST00000116444.2|Hpca|ENSMUSG00000028785.6|hippocalcin
mm10_v2_chr19_+_46396885_46397004	0.925522	Msx2_Hoxd4	ENSMUST00000039922.6|Sufu|ENSMUSG00000025231.10|suppressor of fused homolog (Drosophila) 	ENSMUST00000111867.2|Sufu|ENSMUSG00000025231.10|suppressor of fused homolog (Drosophila) 	ENSMUST00000120778.1|Sufu|ENSMUSG00000025231.10|suppressor of fused homolog (Drosophila)
mm10_v2_chr13_+_51408618_51408781	0.925391	Msx2_Hoxd4	ENSMUST00000087978.3|S1pr3|ENSMUSG00000067586.3|sphingosine-1-phosphate receptor 3
mm10_v2_chr16_+_14705832_14705858	0.915976	Msx2_Hoxd4	ENSMUST00000023356.6|Snai2|ENSMUSG00000022676.6|snail homolog 2 (Drosophila)
mm10_v2_chr7_-_121074501_121074530	0.894865	Msx2_Hoxd4	ENSMUST00000047194.2|Igsf6|ENSMUSG00000035004.2|immunoglobulin superfamily, member 6
mm10_v2_chr18_+_37320374_37320401	0.894362	Msx2_Hoxd4	ENSMUST00000078271.2|Pcdhb5|ENSMUSG00000063687.2|protocadherin beta 5
mm10_v2_chr3_+_84952146_84952186	0.892206	Msx2_Hoxd4	ENSMUST00000029727.7|Fbxw7|ENSMUSG00000028086.8|F-box and WD-40 domain protein 7
mm10_v2_chr4_-_82850721_82850814	0.875662	Msx2_Hoxd4	ENSMUST00000139401.1|Zdhhc21|ENSMUSG00000028403.9|zinc finger, DHHC domain containing 21
mm10_v2_chr2_-_45112890_45113010	0.860966	Msx2_Hoxd4	ENSMUST00000076836.6|Zeb2|ENSMUSG00000026872.10|zinc finger E-box binding homeobox 2
mm10_v2_chr17_-_46327949_46327987	0.858598	Msx2_Hoxd4	ENSMUST00000047970.7|Abcc10|ENSMUSG00000032842.7|ATP-binding cassette, sub-family C (CFTR/MRP), member 10
mm10_v2_chrM_-_14060_14074	0.841215	Msx2_Hoxd4	ENSMUST00000082419.1|mt-Nd6|ENSMUSG00000064368.1|mitochondrially encoded NADH dehydrogenase 6
mm10_v2_chr18_+_37513652_37513652	0.829744	Msx2_Hoxd4	ENSMUST00000061405.4|Pcdhb21|ENSMUSG00000044022.4|protocadherin beta 21
mm10_v2_chr13_-_95250166_95250336	0.827656	Msx2_Hoxd4	ENSMUST00000162153.1|Pde8b|ENSMUSG00000021684.10|phosphodiesterase 8B 	ENSMUST00000160957.2|Pde8b|ENSMUSG00000021684.10|phosphodiesterase 8B 	ENSMUST00000159598.1|Pde8b|ENSMUSG00000021684.10|phosphodiesterase 8B 	ENSMUST00000162412.1|Pde8b|ENSMUSG00000021684.10|phosphodiesterase 8B
mm10_v2_chr3_+_144570687_144570721	0.796006	Msx2_Hoxd4	ENSMUST00000106211.1|Sep15|ENSMUSG00000037072.9|selenoprotein
mm10_v2_chr14_+_115042752_115042879	0.774698	Msx2_Hoxd4	ENSMUST00000134140.2|Mir17hg|ENSMUSG00000089726.2|Mir17 host gene 1 (non-protein coding)
mm10_v2_chr3_+_144570409_144570490	0.770282	Msx2_Hoxd4	ENSMUST00000082437.3|Sep15|ENSMUSG00000037072.9|selenoprotein
mm10_v2_chr1_-_24612700_24612700	0.760709	Msx2_Hoxd4	ENSMUST00000088336.1|Gm10222|ENSMUSG00000067736.1|predicted gene 10222
mm10_v2_chr10_+_128303322_128303352	0.746573	Msx2_Hoxd4	ENSMUST00000005825.6|Pan2|ENSMUSG00000005682.8|PAN2 polyA specific ribonuclease subunit homolog (S. cerevisiae)
mm10_v2_chr15_-_37458523_37458581	0.745227	Msx2_Hoxd4	ENSMUST00000116445.2|Ncald|ENSMUSG00000051359.8|neurocalcin delta
mm10_v2_chrX_-_8132770_8132857	0.744209	Msx2_Hoxd4	ENSMUST00000130832.1|Wdr13|ENSMUSG00000031166.7|WD repeat domain 13 	ENSMUST00000033506.6|Wdr13|ENSMUSG00000031166.7|WD repeat domain 13 	ENSMUST00000115623.1|Wdr13|ENSMUSG00000031166.7|WD repeat domain 13 	ENSMUST00000153839.1|Wdr13|ENSMUSG00000031166.7|WD repeat domain 13
mm10_v2_chr1_+_157458554_157458597	0.739871	Msx2_Hoxd4	ENSMUST00000046743.4|BC026585|ENSMUSG00000033488.5|cDNA sequence BC026585 	ENSMUST00000119891.1|BC026585|ENSMUSG00000033488.5|cDNA sequence BC026585
mm10_v2_chr15_+_41830921_41831001	0.733385	Msx2_Hoxd4	ENSMUST00000166917.1|Oxr1|ENSMUSG00000022307.9|oxidation resistance 1
mm10_v2_chr9_-_89705017_89705068	0.731395	Msx2_Hoxd4	ENSMUST00000058488.6|Tmed3|ENSMUSG00000032353.7|transmembrane emp24 domain containing 3
mm10_v2_chr18_+_37518341_37518359	0.725725	Msx2_Hoxd4	ENSMUST00000097609.1|Pcdhb22|ENSMUSG00000073591.3|protocadherin beta 22
mm10_v2_chrM_+_9870_9885	0.719877	Msx2_Hoxd4	ENSMUST00000084013.1|mt-Nd4l|ENSMUSG00000065947.3|mitochondrially encoded NADH dehydrogenase 4L
mm10_v2_chr7_-_45921418_45921447	0.719659	Msx2_Hoxd4	ENSMUST00000038876.5|Emp3|ENSMUSG00000040212.5|epithelial membrane protein 3
mm10_v2_chr4_-_149126688_149126763	0.708789	Msx2_Hoxd4	ENSMUST00000030815.2|Cort|ENSMUSG00000028971.4|cortistatin
mm10_v2_chr7_-_45920830_45920883	0.696762	Msx2_Hoxd4	ENSMUST00000164119.1|Emp3|ENSMUSG00000040212.5|epithelial membrane protein 3
mm10_v2_chr17_-_90088343_90088373	0.68578	Msx2_Hoxd4	ENSMUST00000173917.1|Nrxn1|ENSMUSG00000024109.12|neurexin I
mm10_v2_chr5_-_84417359_84417389	0.67459	Msx2_Hoxd4	ENSMUST00000113401.1|Epha5|ENSMUSG00000029245.10|Eph receptor A5
mm10_v2_chr4_-_141078302_141078357	0.673232	Msx2_Hoxd4	ENSMUST00000030760.8|Necap2|ENSMUSG00000028923.8|NECAP endocytosis associated 2
mm10_v2_chr6_+_136518820_136518851	0.648252	Msx2_Hoxd4	ENSMUST00000032335.6|Atf7ip|ENSMUSG00000030213.6|activating transcription factor 7 interacting protein
mm10_v2_chr8_-_70527645_70527783	0.62153	Msx2_Hoxd4	ENSMUST00000132867.1|Kxd1|ENSMUSG00000055553.10|KxDL motif containing 1
mm10_v2_chrM_+_10167_10167	0.61915	Msx2_Hoxd4	ENSMUST00000082414.1|mt-Nd4|ENSMUSG00000064363.1|mitochondrially encoded NADH dehydrogenase 4
mm10_v2_chr10_+_39612934_39612934	0.617315	Msx2_Hoxd4	ENSMUST00000019987.6|Traf3ip2|ENSMUSG00000019842.6|TRAF3 interacting protein 2
mm10_v2_chr14_+_54259227_54259241	0.60771	Msx2_Hoxd4	ENSMUST00000041197.7|Abhd4|ENSMUSG00000040997.7|abhydrolase domain containing 4
mm10_v2_chr2_-_45110336_45110487	0.600598	Msx2_Hoxd4	ENSMUST00000028229.6|Zeb2|ENSMUSG00000026872.10|zinc finger E-box binding homeobox 2 	ENSMUST00000152232.1|Zeb2|ENSMUSG00000026872.10|zinc finger E-box binding homeobox 2
mm10_v2_chr15_+_85510812_85510812	0.558984	Msx2_Hoxd4	ENSMUST00000079690.2|Gm4825|ENSMUSG00000063548.2|predicted pseudogene 4825
mm10_v2_chr3_+_19957037_19957073	0.507147	Msx2_Hoxd4	ENSMUST00000091309.5|Cp|ENSMUSG00000003617.10|ceruloplasmin 	ENSMUST00000108329.1|Cp|ENSMUSG00000003617.10|ceruloplasmin 	ENSMUST00000003714.6|Cp|ENSMUSG00000003617.10|ceruloplasmin
mm10_v2_chr10_-_14718191_14718228	0.505854	Msx2_Hoxd4	ENSMUST00000020016.4|Gje1|ENSMUSG00000019867.4|gap junction protein, epsilon 1
mm10_v2_chr2_-_60125651_60125775	0.501438	Msx2_Hoxd4	ENSMUST00000112550.1|Baz2b|ENSMUSG00000026987.10|bromodomain adjacent to zinc finger domain, 2B
mm10_v2_chr3_-_144570136_144570227	0.501315	Msx2_Hoxd4	ENSMUST00000043325.7|Hs2st1|ENSMUSG00000040151.8|heparan sulfate 2-O-sulfotransferase 1
mm10_v2_chr7_-_38019505_38019552	0.496439	Msx2_Hoxd4	ENSMUST00000085513.4|Uri1|ENSMUSG00000030421.8|URI1, prefoldin-like chaperone
mm10_v2_chr13_+_76098734_76098809	0.488303	Msx2_Hoxd4	ENSMUST00000091466.3|Ttc37|ENSMUSG00000033991.8|tetratricopeptide repeat domain 37
mm10_v2_chr15_-_50890396_50890463	0.484733	Msx2_Hoxd4	ENSMUST00000185183.1|Trps1|ENSMUSG00000038679.10|trichorhinophalangeal syndrome I (human)
mm10_v2_chr12_-_85374696_85374719	0.476954	Msx2_Hoxd4	ENSMUST00000040766.7|Tmed10|ENSMUSG00000021248.8|transmembrane emp24-like trafficking protein 10 (yeast)
mm10_v2_chr2_+_76650264_76650278	0.456308	Msx2_Hoxd4	ENSMUST00000099986.2|Dfnb59|ENSMUSG00000075267.3|deafness, autosomal recessive 59 (human)
mm10_v2_chr7_-_84679346_84679401	0.45569	Msx2_Hoxd4	ENSMUST00000069537.2|Zfand6|ENSMUSG00000030629.8|zinc finger, AN1-type domain 6 	ENSMUST00000178385.1|Zfand6|ENSMUSG00000030629.8|zinc finger, AN1-type domain 6
mm10_v2_chr2_-_176144697_176144697	0.45055	Msx2_Hoxd4	ENSMUST00000178872.1|Gm2004|ENSMUSG00000095648.1|predicted gene 2004
mm10_v2_chr6_-_136171722_136171849	0.435342	Msx2_Hoxd4	ENSMUST00000053880.6|Grin2b|ENSMUSG00000030209.8|glutamate receptor, ionotropic, NMDA2B (epsilon 2)
mm10_v2_chrM_+_2743_2761	0.427047	Msx2_Hoxd4	ENSMUST00000082392.1|mt-Nd1|ENSMUSG00000064341.1|mitochondrially encoded NADH dehydrogenase 1
mm10_v2_chr7_+_65693417_65693446	0.421992	Msx2_Hoxd4	ENSMUST00000032726.7|Tm2d3|ENSMUSG00000078681.4|TM2 domain containing 3 	ENSMUST00000107495.3|Tm2d3|ENSMUSG00000078681.4|TM2 domain containing 3
mm10_v2_chr13_-_75943812_75943950	0.421336	Msx2_Hoxd4	ENSMUST00000022078.5|Rhobtb3|ENSMUSG00000021589.6|Rho-related BTB domain containing 3 	ENSMUST00000109606.1|Rhobtb3|ENSMUSG00000021589.6|Rho-related BTB domain containing 3
mm10_v2_chr12_+_74297474_74297474	0.420794	Msx2_Hoxd4	ENSMUST00000072100.3|Dbpht2|ENSMUSG00000029878.5|DNA binding protein with his-thr domain
mm10_v2_chr11_+_103133333_103133359	0.414484	Msx2_Hoxd4	ENSMUST00000124928.1|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2 	ENSMUST00000062530.4|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2
mm10_v2_chr17_+_45506825_45506857	0.412525	Msx2_Hoxd4	ENSMUST00000024733.7|Aars2|ENSMUSG00000023938.7|alanyl-tRNA synthetase 2, mitochondrial (putative)
mm10_v2_chr1_+_180109192_180109265	0.398777	Msx2_Hoxd4	ENSMUST00000143176.1|Cdc42bpa|ENSMUSG00000026490.11|CDC42 binding protein kinase alpha 	ENSMUST00000135056.1|Cdc42bpa|ENSMUSG00000026490.11|CDC42 binding protein kinase alpha
mm10_v2_chr6_+_124304646_124304671	0.393262	Msx2_Hoxd4	ENSMUST00000112541.2|Cd163|ENSMUSG00000008845.3|CD163 antigen 	ENSMUST00000032234.2|Cd163|ENSMUSG00000008845.3|CD163 antigen
mm10_v2_chr2_+_125136692_125136769	0.376551	Msx2_Hoxd4	ENSMUST00000099452.2|Ctxn2|ENSMUSG00000074872.2|cortexin 2
mm10_v2_chr5_-_23616528_23616597	0.369638	Msx2_Hoxd4	ENSMUST00000088392.4|Srpk2|ENSMUSG00000062604.7|serine/arginine-rich protein specific kinase 2
mm10_v2_chr10_+_75037066_75037100	0.363599	Msx2_Hoxd4	ENSMUST00000147802.1|Rab36|ENSMUSG00000020175.7|RAB36, member RAS oncogene family 	ENSMUST00000020391.5|Rab36|ENSMUSG00000020175.7|RAB36, member RAS oncogene family
mm10_v2_chr1_+_191025350_191025350	0.359399	Msx2_Hoxd4	ENSMUST00000181050.1|A230020J21Rik|ENSMUSG00000097845.1|RIKEN cDNA A230020J21 gene
mm10_v2_chr7_+_65693447_65693477	0.357226	Msx2_Hoxd4	ENSMUST00000143508.1|Tm2d3|ENSMUSG00000078681.4|TM2 domain containing 3
mm10_v2_chr7_+_126950687_126950729	0.323341	Msx2_Hoxd4	ENSMUST00000106333.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2
mm10_v2_chr1_+_63176818_63176919	0.310968	Msx2_Hoxd4	ENSMUST00000129339.1|Eef1b2|ENSMUSG00000025967.10|eukaryotic translation elongation factor 1 beta 2
mm10_v2_chr7_-_101845300_101845339	0.30453	Msx2_Hoxd4	ENSMUST00000094141.5|Folr2|ENSMUSG00000032725.9|folate receptor 2 (fetal)
mm10_v2_chr2_+_132847719_132847743	0.295586	Msx2_Hoxd4	ENSMUST00000124836.1|Crls1|ENSMUSG00000027357.10|cardiolipin synthase 1 	ENSMUST00000154160.1|Crls1|ENSMUSG00000027357.10|cardiolipin synthase 1
mm10_v2_chr19_-_53371766_53371766	0.293044	Msx2_Hoxd4	ENSMUST00000086887.1|Gm10197|ENSMUSG00000067085.1|predicted gene 10197
mm10_v2_chr6_+_29361410_29361461	0.287598	Msx2_Hoxd4	ENSMUST00000156163.1|Calu|ENSMUSG00000029767.10|calumenin
mm10_v2_chrX_-_94123359_94123412	0.283615	Msx2_Hoxd4	ENSMUST00000137853.1|Zfx|ENSMUSG00000079509.4|zinc finger protein X-linked 	ENSMUST00000088102.5|Zfx|ENSMUSG00000079509.4|zinc finger protein X-linked 	ENSMUST00000113927.1|Zfx|ENSMUSG00000079509.4|zinc finger protein X-linked
mm10_v2_chrX_-_74246534_74246556	0.282941	Msx2_Hoxd4	ENSMUST00000101454.2|Flna|ENSMUSG00000031328.9|filamin, alpha 	ENSMUST00000033699.6|Flna|ENSMUSG00000031328.9|filamin, alpha
mm10_v2_chrX_-_150814265_150814345	0.278919	Msx2_Hoxd4	ENSMUST00000026302.6|Maged2|ENSMUSG00000025268.9|melanoma antigen, family D, 2 	ENSMUST00000129768.1|Maged2|ENSMUSG00000025268.9|melanoma antigen, family D, 2 	ENSMUST00000112699.2|Maged2|ENSMUSG00000025268.9|melanoma antigen, family D, 2
mm10_v2_chr7_+_97400003_97400047	0.277389	Msx2_Hoxd4	ENSMUST00000032882.8|Ndufc2|ENSMUSG00000030647.8|NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2
mm10_v2_chr4_-_62519885_62519967	0.263456	Msx2_Hoxd4	ENSMUST00000107444.1|Alad|ENSMUSG00000028393.4|aminolevulinate, delta-, dehydratase 	ENSMUST00000030090.3|Alad|ENSMUSG00000028393.4|aminolevulinate, delta-, dehydratase
mm10_v2_chr6_-_124779686_124779742	0.255786	Msx2_Hoxd4	ENSMUST00000147669.1|Lrrc23|ENSMUSG00000030125.5|leucine rich repeat containing 23 	ENSMUST00000128697.1|Lrrc23|ENSMUSG00000030125.5|leucine rich repeat containing 23 	ENSMUST00000032218.3|Lrrc23|ENSMUSG00000030125.5|leucine rich repeat containing 23 	ENSMUST00000112475.2|Lrrc23|ENSMUSG00000030125.5|leucine rich repeat containing 23
mm10_v2_chr10_+_115569986_115570035	0.245611	Msx2_Hoxd4	ENSMUST00000173620.1|A930009A15Rik|ENSMUSG00000092210.1|RIKEN cDNA A930009A15 gene
mm10_v2_chr17_-_14694223_14694262	0.228712	Msx2_Hoxd4	ENSMUST00000170872.1|Thbs2|ENSMUSG00000023885.8|thrombospondin 2
mm10_v2_chr11_-_109472611_109472688	0.228361	Msx2_Hoxd4	ENSMUST00000168740.1|Slc16a6|ENSMUSG00000041920.8|solute carrier family 16 (monocarboxylic acid transporters), member 6
mm10_v2_chr13_+_40859768_40859822	0.228344	Msx2_Hoxd4	ENSMUST00000110191.2|Gcnt2|ENSMUSG00000021360.9|glucosaminyl (N-acetyl) transferase 2, I-branching enzyme
mm10_v2_chr7_+_126950837_126950966	0.226993	Msx2_Hoxd4	ENSMUST00000106332.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2
mm10_v2_chr2_+_180710117_180710201	0.224443	Msx2_Hoxd4	ENSMUST00000029090.2|Gid8|ENSMUSG00000027573.5|GID complex subunit 8 homolog (S. cerevisiae)
mm10_v2_chr7_-_29906524_29906572	0.211069	Msx2_Hoxd4	ENSMUST00000159920.1|Zfp27|ENSMUSG00000062040.8|zinc finger protein 27 	ENSMUST00000162592.1|Zfp27|ENSMUSG00000062040.8|zinc finger protein 27
mm10_v2_chrM_+_7759_7927	0.202132	Msx2_Hoxd4	ENSMUST00000082407.1|mt-Atp8|ENSMUSG00000064356.3|mitochondrially encoded ATP synthase 8 	ENSMUST00000082408.1|mt-Atp6|ENSMUSG00000064357.1|mitochondrially encoded ATP synthase 6
mm10_v2_chr18_+_59062462_59062538	0.201153	Msx2_Hoxd4	ENSMUST00000058633.2|A730017C20Rik|ENSMUSG00000050875.5|RIKEN cDNA A730017C20 gene 	ENSMUST00000175897.1|A730017C20Rik|ENSMUSG00000050875.5|RIKEN cDNA A730017C20 gene 	ENSMUST00000118510.1|A730017C20Rik|ENSMUSG00000050875.5|RIKEN cDNA A730017C20 gene 	ENSMUST00000175830.1|A730017C20Rik|ENSMUSG00000050875.5|RIKEN cDNA A730017C20 gene
mm10_v2_chr1_-_186749304_186749358	0.199813	Msx2_Hoxd4	ENSMUST00000001339.5|Rrp15|ENSMUSG00000001305.5|ribosomal RNA processing 15 homolog (S. cerevisiae)
mm10_v2_chr9_-_107770945_107771007	0.146294	Msx2_Hoxd4	ENSMUST00000183248.1|Rbm5|ENSMUSG00000032580.6|RNA binding motif protein 5 	ENSMUST00000182022.1|Rbm5|ENSMUSG00000032580.6|RNA binding motif protein 5 	ENSMUST00000035199.6|Rbm5|ENSMUSG00000032580.6|RNA binding motif protein 5 	ENSMUST00000182659.1|Rbm5|ENSMUSG00000032580.6|RNA binding motif protein 5
mm10_v2_chr12_-_27160311_27160476	0.133577	Msx2_Hoxd4	ENSMUST00000182473.1|Gm9866|ENSMUSG00000094002.2|predicted gene 9866 	ENSMUST00000177636.1|Gm9866|ENSMUSG00000094002.2|predicted gene 9866 	ENSMUST00000183238.1|Gm9866|ENSMUSG00000094002.2|predicted gene 9866
mm10_v2_chr1_-_133661318_133661386	0.129472	Msx2_Hoxd4	ENSMUST00000179598.1|Zbed6|ENSMUSG00000094410.1|zinc finger, BED domain containing 6 	ENSMUST00000027736.6|Zc3h11a|ENSMUSG00000026464.6|zinc finger CCCH type containing 11A
mm10_v2_chr9_-_50739365_50739517	0.121481	Msx2_Hoxd4	ENSMUST00000117093.1|Dixdc1|ENSMUSG00000032064.11|DIX domain containing 1 	ENSMUST00000121634.1|Dixdc1|ENSMUSG00000032064.11|DIX domain containing 1
mm10_v2_chr4_-_99829180_99829191	0.115839	Msx2_Hoxd4	ENSMUST00000146258.1|Itgb3bp|ENSMUSG00000028549.11|integrin beta 3 binding protein (beta3-endonexin)
mm10_v2_chr13_+_49544443_49544533	0.113027	Msx2_Hoxd4	ENSMUST00000177948.1|Aspn|ENSMUSG00000021388.7|asporin 	ENSMUST00000021820.6|Aspn|ENSMUSG00000021388.7|asporin
mm10_v2_chr7_+_126950518_126950584	0.109914	Msx2_Hoxd4	ENSMUST00000106335.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2 	ENSMUST00000146017.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2
mm10_v2_chr9_-_77544829_77544862	0.108712	Msx2_Hoxd4	ENSMUST00000183734.1|Lrrc1|ENSMUSG00000032352.9|leucine rich repeat containing 1
mm10_v2_chr10_+_127421208_127421235	0.106977	Msx2_Hoxd4	ENSMUST00000168780.1|R3hdm2|ENSMUSG00000025404.9|R3H domain containing 2
mm10_v2_chr1_+_33908172_33908225	0.102836	Msx2_Hoxd4	ENSMUST00000182513.1|Dst|ENSMUSG00000026131.11|dystonin 	ENSMUST00000183034.1|Dst|ENSMUSG00000026131.11|dystonin
mm10_v2_chr4_-_148159838_148159930	0.0960714	Msx2_Hoxd4	ENSMUST00000151127.1|Fbxo44|ENSMUSG00000029001.9|F-box protein 44 	ENSMUST00000105705.2|Fbxo44|ENSMUSG00000029001.9|F-box protein 44
mm10_v2_chr9_-_77544870_77544914	0.0938861	Msx2_Hoxd4	ENSMUST00000183873.1|Lrrc1|ENSMUSG00000032352.9|leucine rich repeat containing 1
mm10_v2_chr4_-_148160031_148160083	0.0936578	Msx2_Hoxd4	ENSMUST00000057907.3|Fbxo44|ENSMUSG00000029001.9|F-box protein 44
mm10_v2_chr5_-_31180110_31180158	0.0774169	Msx2_Hoxd4	ENSMUST00000043161.6|Gtf3c2|ENSMUSG00000029144.10|general transcription factor IIIC, polypeptide 2, beta 	ENSMUST00000088010.5|Gtf3c2|ENSMUSG00000029144.10|general transcription factor IIIC, polypeptide 2, beta
mm10_v2_chr5_-_31179901_31179942	0.0749861	Msx2_Hoxd4	ENSMUST00000101411.2|Gtf3c2|ENSMUSG00000029144.10|general transcription factor IIIC, polypeptide 2, beta 	ENSMUST00000140793.1|Gtf3c2|ENSMUSG00000029144.10|general transcription factor IIIC, polypeptide 2, beta
mm10_v2_chr10_+_5593718_5593739	0.0553231	Msx2_Hoxd4	ENSMUST00000051809.8|Myct1|ENSMUSG00000046916.8|myc target 1
mm10_v2_chr3_+_106113229_106113390	0.0525203	Msx2_Hoxd4	ENSMUST00000079132.5|Chia|ENSMUSG00000062778.6|chitinase, acidic 	ENSMUST00000139086.1|Chia|ENSMUSG00000062778.6|chitinase, acidic
mm10_v2_chr2_+_109280738_109280798	0.0329753	Msx2_Hoxd4	ENSMUST00000028527.7|Kif18a|ENSMUSG00000027115.8|kinesin family member 18A
mm10_v2_chr2_+_155751117_155751284	0.0306088	Msx2_Hoxd4	ENSMUST00000029140.5|Procr|ENSMUSG00000027611.6|protein C receptor, endothelial 	ENSMUST00000132608.1|Procr|ENSMUSG00000027611.6|protein C receptor, endothelial
mm10_v2_chr17_+_46161021_46161072	0.0239781	Msx2_Hoxd4	ENSMUST00000024748.7|Gtpbp2|ENSMUSG00000023952.7|GTP binding protein 2 	ENSMUST00000172170.1|Gtpbp2|ENSMUSG00000023952.7|GTP binding protein 2
mm10_v2_chr8_+_70527724_70527766	0.0227313	Msx2_Hoxd4	ENSMUST00000119353.2|Fkbp8|ENSMUSG00000019428.10|FK506 binding protein 8 	ENSMUST00000075491.7|Fkbp8|ENSMUSG00000019428.10|FK506 binding protein 8
mm10_v2_chr18_+_34840575_34840589	0.0202943	Msx2_Hoxd4	ENSMUST00000043484.7|Reep2|ENSMUSG00000038555.7|receptor accessory protein 2
mm10_v2_chr7_+_144838590_144838614	0.0161509	Msx2_Hoxd4	ENSMUST00000105898.1|Fgf3|ENSMUSG00000031074.8|fibroblast growth factor 3
mm10_v2_chr12_-_76177251_76177265	0.0161456	Msx2_Hoxd4	ENSMUST00000101291.3|Esr2|ENSMUSG00000021055.7|estrogen receptor 2 (beta) 	ENSMUST00000076634.4|Esr2|ENSMUSG00000021055.7|estrogen receptor 2 (beta)
mm10_v2_chr5_+_48242549_48242549	0.00923691	Msx2_Hoxd4	ENSMUST00000172493.1|Slit2|ENSMUSG00000031558.9|slit homolog 2 (Drosophila)
mm10_v2_chr6_-_106800051_106800095	0.0062876	Msx2_Hoxd4	ENSMUST00000013882.7|Crbn|ENSMUSG00000005362.8|cereblon 	ENSMUST00000049675.4|Crbn|ENSMUSG00000005362.8|cereblon 	ENSMUST00000113239.3|Crbn|ENSMUSG00000005362.8|cereblon
mm10_v2_chr9_-_55919605_55919605	0.00420749	Msx2_Hoxd4	ENSMUST00000037408.8|Scaper|ENSMUSG00000034007.9|S phase cyclin A-associated protein in the ER
