mm10_v2_chr5_-_62765618_62765656	0.349238	Msx2_Hoxd4	ENSMUST00000159470.1|Arap2|ENSMUSG00000037999.9|ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2
mm10_v2_chr6_+_41538218_41538218	0.297678	Msx2_Hoxd4	ENSMUST00000103291.1|Trbc1|ENSMUSG00000076490.1|T cell receptor beta, constant region 1
mm10_v2_chr13_-_3945349_3945349	0.242817	Msx2_Hoxd4	ENSMUST00000058610.7|Ucn3|ENSMUSG00000044988.7|urocortin 3
mm10_v2_chrX_-_162964557_162964599	0.231885	Msx2_Hoxd4	ENSMUST00000038769.2|S100g|ENSMUSG00000040808.4|S100 calcium binding protein G
mm10_v2_chr6_+_29853746_29853790	0.22582	Msx2_Hoxd4	ENSMUST00000064872.6|Ahcyl2|ENSMUSG00000029772.11|S-adenosylhomocysteine hydrolase-like 2 	ENSMUST00000152581.1|Ahcyl2|ENSMUSG00000029772.11|S-adenosylhomocysteine hydrolase-like 2 	ENSMUST00000176265.1|Ahcyl2|ENSMUSG00000029772.11|S-adenosylhomocysteine hydrolase-like 2 	ENSMUST00000154079.1|Ahcyl2|ENSMUSG00000029772.11|S-adenosylhomocysteine hydrolase-like 2
mm10_v2_chr5_+_20702129_20702277	0.225451	Msx2_Hoxd4	ENSMUST00000101556.4|Magi2|ENSMUSG00000073174.4|membrane associated guanylate kinase, WW and PDZ domain containing 2
mm10_v2_chr5_+_87925579_87925621	0.176147	Msx2_Hoxd4	ENSMUST00000001667.6|Csn3|ENSMUSG00000001622.9|casein kappa 	ENSMUST00000113267.1|Csn3|ENSMUSG00000001622.9|casein kappa
mm10_v2_chr6_-_124779686_124779742	0.175213	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_chr7_-_115824699_115824752	0.168697	Msx2_Hoxd4	ENSMUST00000169129.1|Sox6|ENSMUSG00000051910.7|SRY-box containing gene 6
mm10_v2_chr1_+_136683375_136683410	0.165302	Msx2_Hoxd4	ENSMUST00000181524.1|Gm19705|ENSMUSG00000097113.1|predicted gene, 19705
mm10_v2_chr9_-_77544829_77544862	0.164157	Msx2_Hoxd4	ENSMUST00000183734.1|Lrrc1|ENSMUSG00000032352.9|leucine rich repeat containing 1
mm10_v2_chr16_-_44016387_44016436	0.163513	Msx2_Hoxd4	ENSMUST00000036174.3|Gramd1c|ENSMUSG00000036292.7|GRAM domain containing 1C
mm10_v2_chr1_+_157526127_157526153	0.131374	Msx2_Hoxd4	ENSMUST00000111700.1|Sec16b|ENSMUSG00000026589.8|SEC16 homolog B (S. cerevisiae)
mm10_v2_chr4_-_49549523_49549546	0.12618	Msx2_Hoxd4	ENSMUST00000029987.9|Aldob|ENSMUSG00000028307.9|aldolase B, fructose-bisphosphate
mm10_v2_chrX_-_143933089_143933142	0.116771	Msx2_Hoxd4	ENSMUST00000087313.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chr1_-_190170178_190170237	0.107457	Msx2_Hoxd4	ENSMUST00000177288.1|Prox1|ENSMUSG00000010175.7|prospero-related homeobox 1
mm10_v2_chr4_-_129261394_129261406	0.107263	Msx2_Hoxd4	ENSMUST00000145261.1|C77080|ENSMUSG00000050390.6|expressed sequence C77080
mm10_v2_chr7_+_126950518_126950584	0.106392	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_+_64235201_64235201	0.101475	Msx2_Hoxd4	ENSMUST00000039011.3|Uchl4|ENSMUSG00000035337.3|ubiquitin carboxyl-terminal esterase L4
mm10_v2_chr5_-_87569023_87569038	0.0997336	Msx2_Hoxd4	ENSMUST00000113314.2|Sult1d1|ENSMUSG00000029273.10|sulfotransferase family 1D, member 1
mm10_v2_chr15_-_58364148_58364148	0.0987476	Msx2_Hoxd4	ENSMUST00000068515.7|Anxa13|ENSMUSG00000055114.7|annexin A13
mm10_v2_chr13_-_102905740_102905814	0.0979494	Msx2_Hoxd4	ENSMUST00000167462.1|Mast4|ENSMUSG00000034751.9|microtubule associated serine/threonine kinase family member 4
mm10_v2_chr13_+_23555023_23555039	0.097083	Msx2_Hoxd4	ENSMUST00000045301.6|Hist1h1d|ENSMUSG00000052565.5|histone cluster 1, H1d
mm10_v2_chr4_-_82850721_82850814	0.0921969	Msx2_Hoxd4	ENSMUST00000139401.1|Zdhhc21|ENSMUSG00000028403.9|zinc finger, DHHC domain containing 21
mm10_v2_chr2_-_63184253_63184292	0.0912544	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_chr9_-_77544870_77544914	0.0885346	Msx2_Hoxd4	ENSMUST00000183873.1|Lrrc1|ENSMUSG00000032352.9|leucine rich repeat containing 1
mm10_v2_chr3_+_40800778_40800786	0.088232	Msx2_Hoxd4	ENSMUST00000169566.1|Plk4|ENSMUSG00000025758.5|polo-like kinase 4
mm10_v2_chr1_-_172632931_172632974	0.0881866	Msx2_Hoxd4	ENSMUST00000027826.5|Dusp23|ENSMUSG00000026544.5|dual specificity phosphatase 23
mm10_v2_chr4_-_62519885_62519967	0.0854728	Msx2_Hoxd4	ENSMUST00000107444.1|Alad|ENSMUSG00000028393.4|aminolevulinate, delta-, dehydratase 	ENSMUST00000030090.3|Alad|ENSMUSG00000028393.4|aminolevulinate, delta-, dehydratase
mm10_v2_chr10_+_39612934_39612934	0.0847669	Msx2_Hoxd4	ENSMUST00000019987.6|Traf3ip2|ENSMUSG00000019842.6|TRAF3 interacting protein 2
mm10_v2_chrX_+_9846945_9846977	0.0845423	Msx2_Hoxd4	ENSMUST00000044987.1|1700054O13Rik|ENSMUSG00000040456.1|RIKEN cDNA 1700054O13 gene
mm10_v2_chr1_-_168432270_168432347	0.0845015	Msx2_Hoxd4	ENSMUST00000072863.4|Pbx1|ENSMUSG00000052534.9|pre B cell leukemia homeobox 1
mm10_v2_chr5_+_87925624_87925639	0.0823374	Msx2_Hoxd4	ENSMUST00000113271.2|Csn3|ENSMUSG00000001622.9|casein kappa
mm10_v2_chrX_-_143933204_143933311	0.0817962	Msx2_Hoxd4	ENSMUST00000112851.1|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000112856.2|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000033642.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chrX_+_101640056_101640108	0.0790925	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_chr2_+_4017727_4017745	0.0768983	Msx2_Hoxd4	ENSMUST00000177457.1|Frmd4a|ENSMUSG00000026657.10|FERM domain containing 4A
mm10_v2_chr9_-_40962333_40962333	0.0762705	Msx2_Hoxd4	ENSMUST00000160120.1|4931429I11Rik|ENSMUSG00000032023.7|RIKEN cDNA 4931429I11 gene
mm10_v2_chr3_-_146495115_146495139	0.0738457	Msx2_Hoxd4	ENSMUST00000093951.2|Spata1|ENSMUSG00000028188.7|spermatogenesis associated 1
mm10_v2_chr6_-_50654438_50654448	0.0738229	Msx2_Hoxd4	ENSMUST00000031853.7|Npvf|ENSMUSG00000029831.7|neuropeptide VF precursor
mm10_v2_chr13_-_102906046_102906111	0.0737051	Msx2_Hoxd4	ENSMUST00000171791.1|Mast4|ENSMUSG00000034751.9|microtubule associated serine/threonine kinase family member 4
mm10_v2_chr2_+_125136692_125136769	0.0735949	Msx2_Hoxd4	ENSMUST00000099452.2|Ctxn2|ENSMUSG00000074872.2|cortexin 2
mm10_v2_chr3_-_85741389_85741389	0.0733708	Msx2_Hoxd4	ENSMUST00000094148.4|Fam160a1|ENSMUSG00000051000.11|family with sequence similarity 160, member A1
mm10_v2_chr3_+_106113229_106113390	0.0733283	Msx2_Hoxd4	ENSMUST00000079132.5|Chia|ENSMUSG00000062778.6|chitinase, acidic 	ENSMUST00000139086.1|Chia|ENSMUSG00000062778.6|chitinase, acidic
mm10_v2_chr15_-_50890396_50890463	0.0719011	Msx2_Hoxd4	ENSMUST00000185183.1|Trps1|ENSMUSG00000038679.10|trichorhinophalangeal syndrome I (human)
mm10_v2_chr7_+_126950837_126950966	0.0689165	Msx2_Hoxd4	ENSMUST00000106332.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2
mm10_v2_chr17_-_46327949_46327987	0.0687673	Msx2_Hoxd4	ENSMUST00000047970.7|Abcc10|ENSMUSG00000032842.7|ATP-binding cassette, sub-family C (CFTR/MRP), member 10
mm10_v2_chr17_-_35046539_35046622	0.0680549	Msx2_Hoxd4	ENSMUST00000007250.7|Msh5|ENSMUSG00000007035.9|mutS homolog 5 (E. coli)
mm10_v2_chr14_-_88471396_88471396	0.0678493	Msx2_Hoxd4	ENSMUST00000061628.5|Pcdh20|ENSMUSG00000050505.6|protocadherin 20
mm10_v2_chr13_+_40859768_40859822	0.0672085	Msx2_Hoxd4	ENSMUST00000110191.2|Gcnt2|ENSMUSG00000021360.9|glucosaminyl (N-acetyl) transferase 2, I-branching enzyme
mm10_v2_chr7_+_126950687_126950729	0.0665954	Msx2_Hoxd4	ENSMUST00000106333.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2
mm10_v2_chr14_+_54259227_54259241	0.0651161	Msx2_Hoxd4	ENSMUST00000041197.7|Abhd4|ENSMUSG00000040997.7|abhydrolase domain containing 4
mm10_v2_chr3_-_144975011_144975046	0.0648867	Msx2_Hoxd4	ENSMUST00000075496.4|Clca6|ENSMUSG00000068547.3|chloride channel calcium activated 6 	ENSMUST00000029923.6|Clca6|ENSMUSG00000068547.3|chloride channel calcium activated 6
mm10_v2_chr8_-_120228221_120228297	0.0647826	Msx2_Hoxd4	ENSMUST00000183235.1|A330074K22Rik|ENSMUSG00000097960.1|RIKEN cDNA A330074K22 gene
mm10_v2_chr11_+_103133303_103133332	0.0618864	Msx2_Hoxd4	ENSMUST00000107037.1|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2
mm10_v2_chr1_+_157458554_157458597	0.0617976	Msx2_Hoxd4	ENSMUST00000046743.4|BC026585|ENSMUSG00000033488.5|cDNA sequence BC026585 	ENSMUST00000119891.1|BC026585|ENSMUSG00000033488.5|cDNA sequence BC026585
mm10_v2_chr6_+_15196949_15197102	0.0585612	Msx2_Hoxd4	ENSMUST00000151301.1|Foxp2|ENSMUSG00000029563.10|forkhead box P2 	ENSMUST00000131414.1|Foxp2|ENSMUSG00000029563.10|forkhead box P2 	ENSMUST00000140557.1|Foxp2|ENSMUSG00000029563.10|forkhead box P2 	ENSMUST00000115469.1|Foxp2|ENSMUSG00000029563.10|forkhead box P2
mm10_v2_chr11_-_109472611_109472688	0.0569879	Msx2_Hoxd4	ENSMUST00000168740.1|Slc16a6|ENSMUSG00000041920.8|solute carrier family 16 (monocarboxylic acid transporters), member 6
mm10_v2_chr10_+_34483400_34483445	0.0565219	Msx2_Hoxd4	ENSMUST00000019913.7|Frk|ENSMUSG00000019779.8|fyn-related kinase 	ENSMUST00000170771.1|Frk|ENSMUSG00000019779.8|fyn-related kinase
mm10_v2_chr5_-_62766153_62766246	0.0554232	Msx2_Hoxd4	ENSMUST00000076623.4|Arap2|ENSMUSG00000037999.9|ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2
mm10_v2_chr9_+_78051938_78051958	0.0523535	Msx2_Hoxd4	ENSMUST00000024104.7|Gcm1|ENSMUSG00000023333.7|glial cells missing homolog 1 (Drosophila)
mm10_v2_chr12_-_76177251_76177265	0.0512946	Msx2_Hoxd4	ENSMUST00000101291.3|Esr2|ENSMUSG00000021055.7|estrogen receptor 2 (beta) 	ENSMUST00000076634.4|Esr2|ENSMUSG00000021055.7|estrogen receptor 2 (beta)
mm10_v2_chr10_-_24092320_24092320	0.0495683	Msx2_Hoxd4	ENSMUST00000092654.2|Taar8b|ENSMUSG00000092113.1|trace amine-associated receptor 8B
mm10_v2_chr17_-_90088343_90088373	0.0494247	Msx2_Hoxd4	ENSMUST00000173917.1|Nrxn1|ENSMUSG00000024109.12|neurexin I
mm10_v2_chr1_+_33908172_33908225	0.0493482	Msx2_Hoxd4	ENSMUST00000182513.1|Dst|ENSMUSG00000026131.11|dystonin 	ENSMUST00000183034.1|Dst|ENSMUSG00000026131.11|dystonin
mm10_v2_chr8_-_8639363_8639363	0.049216	Msx2_Hoxd4	ENSMUST00000152698.1|Efnb2|ENSMUSG00000001300.9|ephrin B2
mm10_v2_chr17_+_17402672_17402771	0.0477657	Msx2_Hoxd4	ENSMUST00000115576.2|Lix1|ENSMUSG00000047786.12|limb expression 1 homolog (chicken)
mm10_v2_chr4_-_40722307_40722398	0.0477462	Msx2_Hoxd4	ENSMUST00000181475.1|Gm6297|ENSMUSG00000097123.1|predicted gene 6297
mm10_v2_chr8_-_61591130_61591148	0.0476164	Msx2_Hoxd4	ENSMUST00000135439.1|Palld|ENSMUSG00000058056.9|palladin, cytoskeletal associated protein 	ENSMUST00000121200.1|Palld|ENSMUSG00000058056.9|palladin, cytoskeletal associated protein
mm10_v2_chr7_-_73537621_73537766	0.046833	Msx2_Hoxd4	ENSMUST00000172704.1|Chd2|ENSMUSG00000078671.4|chromodomain helicase DNA binding protein 2
mm10_v2_chrX_+_159303266_159303281	0.0467189	Msx2_Hoxd4	ENSMUST00000112491.1|Rps6ka3|ENSMUSG00000031309.9|ribosomal protein S6 kinase polypeptide 3
mm10_v2_chr13_+_23695791_23695817	0.0444759	Msx2_Hoxd4	ENSMUST00000041052.2|Hist1h1t|ENSMUSG00000036211.2|histone cluster 1, H1t
mm10_v2_chr4_-_73790602_73790709	0.044402	Msx2_Hoxd4	ENSMUST00000058292.6|Rasef|ENSMUSG00000043003.7|RAS and EF hand domain containing 	ENSMUST00000102837.2|Rasef|ENSMUSG00000043003.7|RAS and EF hand domain containing
mm10_v2_chr11_+_58786139_58786139	0.0432936	Msx2_Hoxd4	ENSMUST00000076393.3|Olfr314|ENSMUSG00000059504.3|olfactory receptor 314
mm10_v2_chr3_+_138065052_138065078	0.0429215	Msx2_Hoxd4	ENSMUST00000163080.2|1110002E22Rik|ENSMUSG00000090066.2|RIKEN cDNA 1110002E22 gene
mm10_v2_chr15_-_37459327_37459380	0.0409925	Msx2_Hoxd4	ENSMUST00000119730.1|Ncald|ENSMUSG00000051359.8|neurocalcin delta 	ENSMUST00000120746.1|Ncald|ENSMUSG00000051359.8|neurocalcin delta
mm10_v2_chr9_-_50739365_50739517	0.0400108	Msx2_Hoxd4	ENSMUST00000117093.1|Dixdc1|ENSMUSG00000032064.11|DIX domain containing 1 	ENSMUST00000121634.1|Dixdc1|ENSMUSG00000032064.11|DIX domain containing 1
mm10_v2_chr1_-_144545320_144545320	0.0397021	Msx2_Hoxd4	ENSMUST00000184189.1|Rgs21|ENSMUSG00000098509.1|regulator of G-protein signalling 21
mm10_v2_chr4_+_101507947_101508032	0.0394904	Msx2_Hoxd4	ENSMUST00000149047.1|Dnajc6|ENSMUSG00000028528.10|DnaJ (Hsp40) homolog, subfamily C, member 6 	ENSMUST00000106929.3|Dnajc6|ENSMUSG00000028528.10|DnaJ (Hsp40) homolog, subfamily C, member 6
mm10_v2_chr18_-_3281752_3281778	0.0379986	Msx2_Hoxd4	ENSMUST00000140332.1|Crem|ENSMUSG00000063889.10|cAMP responsive element modulator 	ENSMUST00000147138.1|Crem|ENSMUSG00000063889.10|cAMP responsive element modulator
mm10_v2_chrX_+_56454871_56454887	0.0364454	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_chr13_+_76098734_76098809	0.0362936	Msx2_Hoxd4	ENSMUST00000091466.3|Ttc37|ENSMUSG00000033991.8|tetratricopeptide repeat domain 37
mm10_v2_chr3_+_52268337_52268388	0.0362045	Msx2_Hoxd4	ENSMUST00000053764.5|Foxo1|ENSMUSG00000044167.5|forkhead box O1
mm10_v2_chr17_-_25785324_25785343	0.0359277	Msx2_Hoxd4	ENSMUST00000150324.1|Haghl|ENSMUSG00000061046.3|hydroxyacylglutathione hydrolase-like
mm10_v2_chr1_+_88306731_88306759	0.0352926	Msx2_Hoxd4	ENSMUST00000040210.7|Trpm8|ENSMUSG00000036251.10|transient receptor potential cation channel, subfamily M, member 8
mm10_v2_chr3_-_79145875_79145930	0.035271	Msx2_Hoxd4	ENSMUST00000118340.1|Rapgef2|ENSMUSG00000062232.8|Rap guanine nucleotide exchange factor (GEF) 2
mm10_v2_chr1_+_60908993_60909033	0.0345091	Msx2_Hoxd4	ENSMUST00000027164.2|Ctla4|ENSMUSG00000026011.7|cytotoxic T-lymphocyte-associated protein 4
mm10_v2_chr1_+_72284367_72284419	0.0343469	Msx2_Hoxd4	ENSMUST00000027380.5|Tmem169|ENSMUSG00000026188.5|transmembrane protein 169 	ENSMUST00000141783.1|Tmem169|ENSMUSG00000026188.5|transmembrane protein 169
mm10_v2_chr19_+_26749726_26749877	0.0339905	Msx2_Hoxd4	ENSMUST00000175842.1|Smarca2|ENSMUSG00000024921.10|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
mm10_v2_chr17_+_79626669_79626697	0.0336219	Msx2_Hoxd4	ENSMUST00000086570.1|4921513D11Rik|ENSMUSG00000066944.1|RIKEN cDNA 4921513D11 gene
mm10_v2_chr6_-_13871477_13871518	0.0333971	Msx2_Hoxd4	ENSMUST00000139231.1|2610001J05Rik|ENSMUSG00000052419.6|RIKEN cDNA 2610001J05 gene
mm10_v2_chr12_+_52516077_52516077	0.0333653	Msx2_Hoxd4	ENSMUST00000110725.1|Arhgap5|ENSMUSG00000035133.8|Rho GTPase activating protein 5
mm10_v2_chr13_+_75967704_75967753	0.0329449	Msx2_Hoxd4	ENSMUST00000022081.1|Spata9|ENSMUSG00000021590.6|spermatogenesis associated 9
mm10_v2_chr6_+_136518820_136518851	0.0322145	Msx2_Hoxd4	ENSMUST00000032335.6|Atf7ip|ENSMUSG00000030213.6|activating transcription factor 7 interacting protein
mm10_v2_chr13_+_23544052_23544052	0.0318867	Msx2_Hoxd4	ENSMUST00000075558.2|Hist1h3f|ENSMUSG00000059309.2|histone cluster 1, H3f
mm10_v2_chr10_+_75037066_75037100	0.030215	Msx2_Hoxd4	ENSMUST00000147802.1|Rab36|ENSMUSG00000020175.7|RAB36, member RAS oncogene family 	ENSMUST00000020391.5|Rab36|ENSMUSG00000020175.7|RAB36, member RAS oncogene family
mm10_v2_chr6_-_131316398_131316398	0.0299458	Msx2_Hoxd4	ENSMUST00000121078.1|Styk1|ENSMUSG00000032899.8|serine/threonine/tyrosine kinase 1
mm10_v2_chr7_-_73541738_73541758	0.0295997	Msx2_Hoxd4	ENSMUST00000169922.2|Chd2|ENSMUSG00000078671.4|chromodomain helicase DNA binding protein 2
mm10_v2_chr19_+_31868754_31868787	0.0289369	Msx2_Hoxd4	ENSMUST00000075838.5|A1cf|ENSMUSG00000052595.6|APOBEC1 complementation factor
mm10_v2_chr14_-_36919314_36919352	0.0282805	Msx2_Hoxd4	ENSMUST00000182797.1|Ccser2|ENSMUSG00000058690.8|coiled-coil serine rich 2
mm10_v2_chr18_-_3281712_3281747	0.0280996	Msx2_Hoxd4	ENSMUST00000182204.1|Crem|ENSMUSG00000063889.10|cAMP responsive element modulator 	ENSMUST00000154705.1|Crem|ENSMUSG00000063889.10|cAMP responsive element modulator 	ENSMUST00000182833.1|Crem|ENSMUSG00000063889.10|cAMP responsive element modulator 	ENSMUST00000151084.1|Crem|ENSMUSG00000063889.10|cAMP responsive element modulator
mm10_v2_chr6_+_37870786_37870882	0.0275345	Msx2_Hoxd4	ENSMUST00000120428.1|Trim24|ENSMUSG00000029833.11|tripartite motif-containing 24 	ENSMUST00000031859.7|Trim24|ENSMUSG00000029833.11|tripartite motif-containing 24
mm10_v2_chr15_-_37458523_37458581	0.0270051	Msx2_Hoxd4	ENSMUST00000116445.2|Ncald|ENSMUSG00000051359.8|neurocalcin delta
mm10_v2_chr6_+_124304646_124304671	0.0255592	Msx2_Hoxd4	ENSMUST00000112541.2|Cd163|ENSMUSG00000008845.3|CD163 antigen 	ENSMUST00000032234.2|Cd163|ENSMUSG00000008845.3|CD163 antigen
mm10_v2_chr9_-_71163224_71163293	0.0253948	Msx2_Hoxd4	ENSMUST00000074465.2|Aqp9|ENSMUSG00000032204.7|aquaporin 9
mm10_v2_chr2_+_180710117_180710201	0.0251986	Msx2_Hoxd4	ENSMUST00000029090.2|Gid8|ENSMUSG00000027573.5|GID complex subunit 8 homolog (S. cerevisiae)
mm10_v2_chr4_-_148159838_148159930	0.0233613	Msx2_Hoxd4	ENSMUST00000151127.1|Fbxo44|ENSMUSG00000029001.9|F-box protein 44 	ENSMUST00000105705.2|Fbxo44|ENSMUSG00000029001.9|F-box protein 44
mm10_v2_chr1_-_133661318_133661386	0.022936	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_chr6_+_13871517_13871569	0.0227447	Msx2_Hoxd4	ENSMUST00000181090.1|1110019D14Rik|ENSMUSG00000097616.1|RIKEN cDNA 1110019D14 gene 	ENSMUST00000181225.1|1110019D14Rik|ENSMUSG00000097616.1|RIKEN cDNA 1110019D14 gene
mm10_v2_chr2_-_63184170_63184195	0.0223799	Msx2_Hoxd4	ENSMUST00000112452.1|Kcnh7|ENSMUSG00000059742.4|potassium voltage-gated channel, subfamily H (eag-related), member 7
mm10_v2_chrX_+_159708593_159708612	0.0220702	Msx2_Hoxd4	ENSMUST00000080394.6|Sh3kbp1|ENSMUSG00000040990.11|SH3-domain kinase binding protein 1
mm10_v2_chr9_-_55919605_55919605	0.022059	Msx2_Hoxd4	ENSMUST00000037408.8|Scaper|ENSMUSG00000034007.9|S phase cyclin A-associated protein in the ER
mm10_v2_chr5_-_146220901_146220987	0.0219541	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_+_101507855_101507871	0.0214968	Msx2_Hoxd4	ENSMUST00000038207.5|Dnajc6|ENSMUSG00000028528.10|DnaJ (Hsp40) homolog, subfamily C, member 6
mm10_v2_chr2_+_80617045_80617290	0.0210799	Msx2_Hoxd4	ENSMUST00000028384.4|Dusp19|ENSMUSG00000027001.4|dual specificity phosphatase 19
mm10_v2_chr1_-_72284248_72284314	0.0210224	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_+_165788746_165788769	0.0196063	Msx2_Hoxd4	ENSMUST00000161559.2|Cd247|ENSMUSG00000005763.9|CD247 antigen
mm10_v2_chr19_-_39740999_39741054	0.0195197	Msx2_Hoxd4	ENSMUST00000099472.3|Cyp2c68|ENSMUSG00000074882.3|cytochrome P450, family 2, subfamily c, polypeptide 68
mm10_v2_chr10_-_25536114_25536272	0.0192101	Msx2_Hoxd4	ENSMUST00000179685.1|Smlr1|ENSMUSG00000096546.1|small leucine-rich protein 1
mm10_v2_chr7_-_34654342_34654398	0.0187573	Msx2_Hoxd4	ENSMUST00000108069.1|Kctd15|ENSMUSG00000030499.3|potassium channel tetramerisation domain containing 15
mm10_v2_chr11_+_103133333_103133359	0.0187478	Msx2_Hoxd4	ENSMUST00000124928.1|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2 	ENSMUST00000062530.4|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2
mm10_v2_chr7_-_101845300_101845339	0.0181509	Msx2_Hoxd4	ENSMUST00000094141.5|Folr2|ENSMUSG00000032725.9|folate receptor 2 (fetal)
mm10_v2_chr15_-_101786458_101786528	0.0178777	Msx2_Hoxd4	ENSMUST00000071104.4|Krt72|ENSMUSG00000056605.6|keratin 72
mm10_v2_chr9_-_107770945_107771007	0.0178303	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_chr5_+_65348386_65348406	0.0177779	Msx2_Hoxd4	ENSMUST00000031096.7|Klb|ENSMUSG00000029195.7|klotho beta
mm10_v2_chr18_+_37513652_37513652	0.0177594	Msx2_Hoxd4	ENSMUST00000061405.4|Pcdhb21|ENSMUSG00000044022.4|protocadherin beta 21
mm10_v2_chr3_+_84952146_84952186	0.0172715	Msx2_Hoxd4	ENSMUST00000029727.7|Fbxw7|ENSMUSG00000028086.8|F-box and WD-40 domain protein 7
mm10_v2_chr1_+_165788681_165788728	0.0167887	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_chr1_-_132390301_132390373	0.0166429	Msx2_Hoxd4	ENSMUST00000132435.1|Tmcc2|ENSMUSG00000042066.9|transmembrane and coiled-coil domains 2
mm10_v2_chr5_-_107875035_107875107	0.0165868	Msx2_Hoxd4	ENSMUST00000138111.1|Evi5|ENSMUSG00000011831.10|ecotropic viral integration site 5 	ENSMUST00000112642.1|Evi5|ENSMUSG00000011831.10|ecotropic viral integration site 5
mm10_v2_chr4_-_3872105_3872105	0.0164726	Msx2_Hoxd4	ENSMUST00000105158.1|Mos|ENSMUSG00000078365.5|Moloney sarcoma oncogene
mm10_v2_chrX_-_103981242_103981287	0.0163751	Msx2_Hoxd4	ENSMUST00000121153.1|Rlim|ENSMUSG00000056537.5|ring finger protein, LIM domain interacting 	ENSMUST00000070705.4|Rlim|ENSMUSG00000056537.5|ring finger protein, LIM domain interacting
mm10_v2_chr2_+_20737306_20737321	0.0152582	Msx2_Hoxd4	ENSMUST00000114606.1|Etl4|ENSMUSG00000036617.10|enhancer trap locus 4 	ENSMUST00000114608.1|Etl4|ENSMUSG00000036617.10|enhancer trap locus 4
mm10_v2_chr10_+_128303322_128303352	0.0150293	Msx2_Hoxd4	ENSMUST00000005825.6|Pan2|ENSMUSG00000005682.8|PAN2 polyA specific ribonuclease subunit homolog (S. cerevisiae)
mm10_v2_chr7_+_65693447_65693477	0.0146828	Msx2_Hoxd4	ENSMUST00000143508.1|Tm2d3|ENSMUSG00000078681.4|TM2 domain containing 3
mm10_v2_chr19_+_46396885_46397004	0.0146331	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_chr12_-_108179210_108179225	0.0143247	Msx2_Hoxd4	ENSMUST00000125916.2|Setd3|ENSMUSG00000056770.9|SET domain containing 3 	ENSMUST00000109879.1|Setd3|ENSMUSG00000056770.9|SET domain containing 3
mm10_v2_chr7_+_123123870_123123901	0.0141061	Msx2_Hoxd4	ENSMUST00000094053.5|Tnrc6a|ENSMUSG00000052707.7|trinucleotide repeat containing 6a
mm10_v2_chr4_-_148160031_148160083	0.0135933	Msx2_Hoxd4	ENSMUST00000057907.3|Fbxo44|ENSMUSG00000029001.9|F-box protein 44
mm10_v2_chr11_-_99322943_99322957	0.013528	Msx2_Hoxd4	ENSMUST00000038004.2|Krt25|ENSMUSG00000035831.2|keratin 25
mm10_v2_chr4_+_3940747_3940854	0.0133852	Msx2_Hoxd4	ENSMUST00000119403.1|Chchd7|ENSMUSG00000042198.6|coiled-coil-helix-coiled-coil-helix domain containing 7
mm10_v2_chr2_-_33428222_33428222	0.0133182	Msx2_Hoxd4	ENSMUST00000091037.2|Zbtb34|ENSMUSG00000068966.4|zinc finger and BTB domain containing 34
mm10_v2_chr12_-_85374696_85374719	0.0128068	Msx2_Hoxd4	ENSMUST00000040766.7|Tmed10|ENSMUSG00000021248.8|transmembrane emp24-like trafficking protein 10 (yeast)
mm10_v2_chr10_-_13324160_13324242	0.0127117	Msx2_Hoxd4	ENSMUST00000105545.4|Phactr2|ENSMUSG00000062866.9|phosphatase and actin regulator 2
mm10_v2_chrX_-_8132770_8132857	0.0118863	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_chr10_+_127421208_127421235	0.0116992	Msx2_Hoxd4	ENSMUST00000168780.1|R3hdm2|ENSMUSG00000025404.9|R3H domain containing 2
mm10_v2_chr11_+_95010277_95010293	0.0114058	Msx2_Hoxd4	ENSMUST00000124735.1|Samd14|ENSMUSG00000047181.6|sterile alpha motif domain containing 14
mm10_v2_chr5_-_23616528_23616597	0.0113657	Msx2_Hoxd4	ENSMUST00000088392.4|Srpk2|ENSMUSG00000062604.7|serine/arginine-rich protein specific kinase 2
mm10_v2_chr7_-_114117761_114117787	0.0113259	Msx2_Hoxd4	ENSMUST00000069449.5|Rras2|ENSMUSG00000055723.5|related RAS viral (r-ras) oncogene homolog 2
mm10_v2_chr6_-_23650298_23650309	0.0107435	Msx2_Hoxd4	ENSMUST00000063548.3|Rnf133|ENSMUSG00000051956.4|ring finger protein 133
mm10_v2_chrX_-_150814265_150814345	0.0105732	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_chr15_+_41830921_41831001	0.0101912	Msx2_Hoxd4	ENSMUST00000166917.1|Oxr1|ENSMUSG00000022307.9|oxidation resistance 1
mm10_v2_chr18_+_68337504_68337603	0.0100616	Msx2_Hoxd4	ENSMUST00000172148.1|Mc5r|ENSMUSG00000007480.3|melanocortin 5 receptor
mm10_v2_chr11_+_78465697_78465735	0.0090444	Msx2_Hoxd4	ENSMUST00000001126.3|Slc46a1|ENSMUSG00000020829.9|solute carrier family 46, member 1
mm10_v2_chr10_-_24101951_24101951	0.00898889	Msx2_Hoxd4	ENSMUST00000170267.1|Taar8c|ENSMUSG00000096204.1|trace amine-associated receptor 8C
mm10_v2_chr6_+_29361410_29361461	0.00875557	Msx2_Hoxd4	ENSMUST00000156163.1|Calu|ENSMUSG00000029767.10|calumenin
mm10_v2_chr11_+_76904513_76904569	0.00851203	Msx2_Hoxd4	ENSMUST00000072633.3|Tmigd1|ENSMUSG00000020839.10|transmembrane and immunoglobulin domain containing 1
mm10_v2_chr6_-_23650206_23650271	0.00826621	Msx2_Hoxd4	ENSMUST00000115354.1|Rnf133|ENSMUSG00000051956.4|ring finger protein 133
mm10_v2_chr7_-_84679346_84679401	0.00815406	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_chr1_+_53061637_53061663	0.00789055	Msx2_Hoxd4	ENSMUST00000027269.5|Mstn|ENSMUSG00000026100.5|myostatin
mm10_v2_chr1_+_180109192_180109265	0.00780259	Msx2_Hoxd4	ENSMUST00000143176.1|Cdc42bpa|ENSMUSG00000026490.11|CDC42 binding protein kinase alpha 	ENSMUST00000135056.1|Cdc42bpa|ENSMUSG00000026490.11|CDC42 binding protein kinase alpha
mm10_v2_chr4_-_141078302_141078357	0.00746657	Msx2_Hoxd4	ENSMUST00000030760.8|Necap2|ENSMUSG00000028923.8|NECAP endocytosis associated 2
mm10_v2_chr12_-_108179237_108179339	0.0063765	Msx2_Hoxd4	ENSMUST00000071095.7|Setd3|ENSMUSG00000056770.9|SET domain containing 3
mm10_v2_chr7_+_144838590_144838614	0.00562555	Msx2_Hoxd4	ENSMUST00000105898.1|Fgf3|ENSMUSG00000031074.8|fibroblast growth factor 3
mm10_v2_chr4_-_119492563_119492628	0.00550802	Msx2_Hoxd4	ENSMUST00000049994.7|Rimkla|ENSMUSG00000048899.8|ribosomal modification protein rimK-like family member A
mm10_v2_chr7_+_96522342_96522398	0.00448982	Msx2_Hoxd4	ENSMUST00000129737.1|Tenm4|ENSMUSG00000048078.10|teneurin transmembrane protein 4
mm10_v2_chr5_+_48242549_48242549	0.00418962	Msx2_Hoxd4	ENSMUST00000172493.1|Slit2|ENSMUSG00000031558.9|slit homolog 2 (Drosophila)
mm10_v2_chr19_-_55241236_55241236	0.00414615	Msx2_Hoxd4	ENSMUST00000069183.6|Gucy2g|ENSMUSG00000055523.6|guanylate cyclase 2g
mm10_v2_chr2_+_35622010_35622063	0.00381917	Msx2_Hoxd4	ENSMUST00000091010.5|Dab2ip|ENSMUSG00000026883.11|disabled 2 interacting protein
mm10_v2_chr2_-_60125651_60125775	0.00354764	Msx2_Hoxd4	ENSMUST00000112550.1|Baz2b|ENSMUSG00000026987.10|bromodomain adjacent to zinc finger domain, 2B
mm10_v2_chr7_-_29906524_29906572	0.00316502	Msx2_Hoxd4	ENSMUST00000159920.1|Zfp27|ENSMUSG00000062040.8|zinc finger protein 27 	ENSMUST00000162592.1|Zfp27|ENSMUSG00000062040.8|zinc finger protein 27
mm10_v2_chr11_+_98798653_98798664	0.00224236	Msx2_Hoxd4	ENSMUST00000037930.6|Msl1|ENSMUSG00000052915.8|male-specific lethal 1 homolog (Drosophila)
mm10_v2_chr12_+_36314160_36314171	0.00186681	Msx2_Hoxd4	ENSMUST00000041407.5|Sostdc1|ENSMUSG00000036169.5|sclerostin domain containing 1
mm10_v2_chr17_+_46161021_46161072	0.00102252	Msx2_Hoxd4	ENSMUST00000024748.7|Gtpbp2|ENSMUSG00000023952.7|GTP binding protein 2 	ENSMUST00000172170.1|Gtpbp2|ENSMUSG00000023952.7|GTP binding protein 2
mm10_v2_chr10_-_14718191_14718228	0.000629938	Msx2_Hoxd4	ENSMUST00000020016.4|Gje1|ENSMUSG00000019867.4|gap junction protein, epsilon 1
