mm10_v2_chr9_-_118014160_118014160	0.391335	Msx2_Hoxd4	ENSMUST00000111769.3|Zcwpw2|ENSMUSG00000032443.9|zinc finger, CW type with PWWP domain 2
mm10_v2_chr13_-_3945349_3945349	0.366122	Msx2_Hoxd4	ENSMUST00000058610.7|Ucn3|ENSMUSG00000044988.7|urocortin 3
mm10_v2_chr11_+_103133333_103133359	0.302939	Msx2_Hoxd4	ENSMUST00000124928.1|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2 	ENSMUST00000062530.4|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2
mm10_v2_chr1_+_72284367_72284419	0.269738	Msx2_Hoxd4	ENSMUST00000027380.5|Tmem169|ENSMUSG00000026188.5|transmembrane protein 169 	ENSMUST00000141783.1|Tmem169|ENSMUSG00000026188.5|transmembrane protein 169
mm10_v2_chr6_-_36811361_36811361	0.257979	Msx2_Hoxd4	ENSMUST00000101534.1|Ptn|ENSMUSG00000029838.8|pleiotrophin
mm10_v2_chr4_-_49549523_49549546	0.239633	Msx2_Hoxd4	ENSMUST00000029987.9|Aldob|ENSMUSG00000028307.9|aldolase B, fructose-bisphosphate
mm10_v2_chr2_+_125136692_125136769	0.22415	Msx2_Hoxd4	ENSMUST00000099452.2|Ctxn2|ENSMUSG00000074872.2|cortexin 2
mm10_v2_chr5_+_20702129_20702277	0.222578	Msx2_Hoxd4	ENSMUST00000101556.4|Magi2|ENSMUSG00000073174.4|membrane associated guanylate kinase, WW and PDZ domain containing 2
mm10_v2_chr10_-_33624587_33624769	0.184544	Msx2_Hoxd4	ENSMUST00000160299.1|Clvs2|ENSMUSG00000019785.7|clavesin 2 	ENSMUST00000019920.6|Clvs2|ENSMUSG00000019785.7|clavesin 2
mm10_v2_chr3_-_146495115_146495139	0.183246	Msx2_Hoxd4	ENSMUST00000093951.2|Spata1|ENSMUSG00000028188.7|spermatogenesis associated 1
mm10_v2_chr7_-_73537621_73537766	0.176715	Msx2_Hoxd4	ENSMUST00000172704.1|Chd2|ENSMUSG00000078671.4|chromodomain helicase DNA binding protein 2
mm10_v2_chr1_+_136683375_136683410	0.176395	Msx2_Hoxd4	ENSMUST00000181524.1|Gm19705|ENSMUSG00000097113.1|predicted gene, 19705
mm10_v2_chr6_+_41538218_41538218	0.162792	Msx2_Hoxd4	ENSMUST00000103291.1|Trbc1|ENSMUSG00000076490.1|T cell receptor beta, constant region 1
mm10_v2_chr1_+_186749368_186749415	0.154476	Msx2_Hoxd4	ENSMUST00000180869.1|A430105J06Rik|ENSMUSG00000097784.1|RIKEN cDNA A430105J06 gene
mm10_v2_chr1_-_190170178_190170237	0.148096	Msx2_Hoxd4	ENSMUST00000177288.1|Prox1|ENSMUSG00000010175.7|prospero-related homeobox 1
mm10_v2_chr4_-_40722307_40722398	0.147195	Msx2_Hoxd4	ENSMUST00000181475.1|Gm6297|ENSMUSG00000097123.1|predicted gene 6297
mm10_v2_chr6_+_29853746_29853790	0.141906	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_chr17_-_90088343_90088373	0.141317	Msx2_Hoxd4	ENSMUST00000173917.1|Nrxn1|ENSMUSG00000024109.12|neurexin I
mm10_v2_chr5_-_87569023_87569038	0.138252	Msx2_Hoxd4	ENSMUST00000113314.2|Sult1d1|ENSMUSG00000029273.10|sulfotransferase family 1D, member 1
mm10_v2_chr4_-_149126688_149126763	0.134931	Msx2_Hoxd4	ENSMUST00000030815.2|Cort|ENSMUSG00000028971.4|cortistatin
mm10_v2_chr10_+_34483400_34483445	0.1308	Msx2_Hoxd4	ENSMUST00000019913.7|Frk|ENSMUSG00000019779.8|fyn-related kinase 	ENSMUST00000170771.1|Frk|ENSMUSG00000019779.8|fyn-related kinase
mm10_v2_chr10_-_24101951_24101951	0.128948	Msx2_Hoxd4	ENSMUST00000170267.1|Taar8c|ENSMUSG00000096204.1|trace amine-associated receptor 8C
mm10_v2_chr16_-_44016387_44016436	0.124397	Msx2_Hoxd4	ENSMUST00000036174.3|Gramd1c|ENSMUSG00000036292.7|GRAM domain containing 1C
mm10_v2_chr1_-_168432270_168432347	0.123779	Msx2_Hoxd4	ENSMUST00000072863.4|Pbx1|ENSMUSG00000052534.9|pre B cell leukemia homeobox 1
mm10_v2_chr11_+_95010277_95010293	0.121925	Msx2_Hoxd4	ENSMUST00000124735.1|Samd14|ENSMUSG00000047181.6|sterile alpha motif domain containing 14
mm10_v2_chr6_+_124304646_124304671	0.121046	Msx2_Hoxd4	ENSMUST00000112541.2|Cd163|ENSMUSG00000008845.3|CD163 antigen 	ENSMUST00000032234.2|Cd163|ENSMUSG00000008845.3|CD163 antigen
mm10_v2_chr5_-_62765618_62765656	0.118431	Msx2_Hoxd4	ENSMUST00000159470.1|Arap2|ENSMUSG00000037999.9|ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2
mm10_v2_chr11_+_59306920_59306935	0.115682	Msx2_Hoxd4	ENSMUST00000000128.3|Wnt9a|ENSMUSG00000000126.5|wingless-type MMTV integration site 9A 	ENSMUST00000108783.3|Wnt9a|ENSMUSG00000000126.5|wingless-type MMTV integration site 9A
mm10_v2_chrX_+_101640056_101640108	0.114874	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_chr11_+_103133303_103133332	0.11427	Msx2_Hoxd4	ENSMUST00000107037.1|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2
mm10_v2_chr10_+_75037066_75037100	0.110159	Msx2_Hoxd4	ENSMUST00000147802.1|Rab36|ENSMUSG00000020175.7|RAB36, member RAS oncogene family 	ENSMUST00000020391.5|Rab36|ENSMUSG00000020175.7|RAB36, member RAS oncogene family
mm10_v2_chr13_+_23555023_23555039	0.109732	Msx2_Hoxd4	ENSMUST00000045301.6|Hist1h1d|ENSMUSG00000052565.5|histone cluster 1, H1d
mm10_v2_chr18_+_37513652_37513652	0.109423	Msx2_Hoxd4	ENSMUST00000061405.4|Pcdhb21|ENSMUSG00000044022.4|protocadherin beta 21
mm10_v2_chr17_+_17402672_17402771	0.106345	Msx2_Hoxd4	ENSMUST00000115576.2|Lix1|ENSMUSG00000047786.12|limb expression 1 homolog (chicken)
mm10_v2_chr3_+_138065052_138065078	0.0999749	Msx2_Hoxd4	ENSMUST00000163080.2|1110002E22Rik|ENSMUSG00000090066.2|RIKEN cDNA 1110002E22 gene
mm10_v2_chr3_-_75270073_75270085	0.0949698	Msx2_Hoxd4	ENSMUST00000039047.4|Serpini2|ENSMUSG00000034139.4|serine (or cysteine) peptidase inhibitor, clade I, member 2
mm10_v2_chr4_-_73790602_73790709	0.0914404	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_chrX_+_159708593_159708612	0.091113	Msx2_Hoxd4	ENSMUST00000080394.6|Sh3kbp1|ENSMUSG00000040990.11|SH3-domain kinase binding protein 1
mm10_v2_chrX_+_56454871_56454887	0.0887109	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_chr2_-_63184253_63184292	0.0878889	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_chr8_+_31111816_31111891	0.0870958	Msx2_Hoxd4	ENSMUST00000046941.7|Rnf122|ENSMUSG00000039328.9|ring finger protein 122
mm10_v2_chr1_+_33908172_33908225	0.0867012	Msx2_Hoxd4	ENSMUST00000182513.1|Dst|ENSMUSG00000026131.11|dystonin 	ENSMUST00000183034.1|Dst|ENSMUSG00000026131.11|dystonin
mm10_v2_chr18_-_3281752_3281778	0.0846581	Msx2_Hoxd4	ENSMUST00000140332.1|Crem|ENSMUSG00000063889.10|cAMP responsive element modulator 	ENSMUST00000147138.1|Crem|ENSMUSG00000063889.10|cAMP responsive element modulator
mm10_v2_chr18_-_3281712_3281747	0.0840688	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_chr7_-_29906524_29906572	0.0828213	Msx2_Hoxd4	ENSMUST00000159920.1|Zfp27|ENSMUSG00000062040.8|zinc finger protein 27 	ENSMUST00000162592.1|Zfp27|ENSMUSG00000062040.8|zinc finger protein 27
mm10_v2_chr12_+_38783503_38783527	0.0806909	Msx2_Hoxd4	ENSMUST00000159334.1|Etv1|ENSMUSG00000004151.10|ets variant gene 1
mm10_v2_chr17_-_46327949_46327987	0.0803215	Msx2_Hoxd4	ENSMUST00000047970.7|Abcc10|ENSMUSG00000032842.7|ATP-binding cassette, sub-family C (CFTR/MRP), member 10
mm10_v2_chr4_+_102570065_102570124	0.08018	Msx2_Hoxd4	ENSMUST00000097950.2|Pde4b|ENSMUSG00000028525.10|phosphodiesterase 4B, cAMP specific
mm10_v2_chr12_+_74297474_74297474	0.0797568	Msx2_Hoxd4	ENSMUST00000072100.3|Dbpht2|ENSMUSG00000029878.5|DNA binding protein with his-thr domain
mm10_v2_chr6_-_124779686_124779742	0.0778753	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_chr6_-_131316398_131316398	0.0750341	Msx2_Hoxd4	ENSMUST00000121078.1|Styk1|ENSMUSG00000032899.8|serine/threonine/tyrosine kinase 1
mm10_v2_chr7_+_126950518_126950584	0.073628	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_chr12_+_36314160_36314171	0.0723235	Msx2_Hoxd4	ENSMUST00000041407.5|Sostdc1|ENSMUSG00000036169.5|sclerostin domain containing 1
mm10_v2_chr3_-_85741389_85741389	0.0722768	Msx2_Hoxd4	ENSMUST00000094148.4|Fam160a1|ENSMUSG00000051000.11|family with sequence similarity 160, member A1
mm10_v2_chr2_+_180710117_180710201	0.0714873	Msx2_Hoxd4	ENSMUST00000029090.2|Gid8|ENSMUSG00000027573.5|GID complex subunit 8 homolog (S. cerevisiae)
mm10_v2_chr13_-_102906046_102906111	0.0701565	Msx2_Hoxd4	ENSMUST00000171791.1|Mast4|ENSMUSG00000034751.9|microtubule associated serine/threonine kinase family member 4
mm10_v2_chr19_+_31868754_31868787	0.0671282	Msx2_Hoxd4	ENSMUST00000075838.5|A1cf|ENSMUSG00000052595.6|APOBEC1 complementation factor
mm10_v2_chr7_-_121074501_121074530	0.0658258	Msx2_Hoxd4	ENSMUST00000047194.2|Igsf6|ENSMUSG00000035004.2|immunoglobulin superfamily, member 6
mm10_v2_chr6_-_13871477_13871518	0.0633844	Msx2_Hoxd4	ENSMUST00000139231.1|2610001J05Rik|ENSMUSG00000052419.6|RIKEN cDNA 2610001J05 gene
mm10_v2_chr5_-_53707532_53707704	0.0604181	Msx2_Hoxd4	ENSMUST00000031093.3|Cckar|ENSMUSG00000029193.4|cholecystokinin A receptor
mm10_v2_chr8_-_70527645_70527783	0.0591262	Msx2_Hoxd4	ENSMUST00000132867.1|Kxd1|ENSMUSG00000055553.10|KxDL motif containing 1
mm10_v2_chrX_-_143933204_143933311	0.0589785	Msx2_Hoxd4	ENSMUST00000112851.1|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000112856.2|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000033642.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chr11_-_109472611_109472688	0.0583435	Msx2_Hoxd4	ENSMUST00000168740.1|Slc16a6|ENSMUSG00000041920.8|solute carrier family 16 (monocarboxylic acid transporters), member 6
mm10_v2_chr11_+_78465697_78465735	0.0580934	Msx2_Hoxd4	ENSMUST00000001126.3|Slc46a1|ENSMUSG00000020829.9|solute carrier family 46, member 1
mm10_v2_chr4_+_141746672_141746759	0.0564731	Msx2_Hoxd4	ENSMUST00000038161.4|Agmat|ENSMUSG00000040706.4|agmatine ureohydrolase (agmatinase)
mm10_v2_chr15_+_92597104_92597121	0.0560401	Msx2_Hoxd4	ENSMUST00000035399.8|Pdzrn4|ENSMUSG00000036218.9|PDZ domain containing RING finger 4
mm10_v2_chr1_-_72284248_72284314	0.0556007	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_chrX_-_150814265_150814345	0.0549385	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_chr5_-_146220901_146220987	0.0545089	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_chr6_+_37870786_37870882	0.0539128	Msx2_Hoxd4	ENSMUST00000120428.1|Trim24|ENSMUSG00000029833.11|tripartite motif-containing 24 	ENSMUST00000031859.7|Trim24|ENSMUSG00000029833.11|tripartite motif-containing 24
mm10_v2_chr13_-_102905740_102905814	0.0532977	Msx2_Hoxd4	ENSMUST00000167462.1|Mast4|ENSMUSG00000034751.9|microtubule associated serine/threonine kinase family member 4
mm10_v2_chr1_+_157458554_157458597	0.0529431	Msx2_Hoxd4	ENSMUST00000046743.4|BC026585|ENSMUSG00000033488.5|cDNA sequence BC026585 	ENSMUST00000119891.1|BC026585|ENSMUSG00000033488.5|cDNA sequence BC026585
mm10_v2_chr15_-_36879816_36879884	0.052625	Msx2_Hoxd4	ENSMUST00000100713.2|Gm10384|ENSMUSG00000072618.2|predicted gene 10384
mm10_v2_chr7_-_45921418_45921447	0.0505589	Msx2_Hoxd4	ENSMUST00000038876.5|Emp3|ENSMUSG00000040212.5|epithelial membrane protein 3
mm10_v2_chr7_+_126950687_126950729	0.0502685	Msx2_Hoxd4	ENSMUST00000106333.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2
mm10_v2_chr18_+_37518341_37518359	0.0501348	Msx2_Hoxd4	ENSMUST00000097609.1|Pcdhb22|ENSMUSG00000073591.3|protocadherin beta 22
mm10_v2_chr19_-_39740999_39741054	0.0497133	Msx2_Hoxd4	ENSMUST00000099472.3|Cyp2c68|ENSMUSG00000074882.3|cytochrome P450, family 2, subfamily c, polypeptide 68
mm10_v2_chr8_+_81856324_81856376	0.0495155	Msx2_Hoxd4	ENSMUST00000109851.2|Inpp4b|ENSMUSG00000037940.9|inositol polyphosphate-4-phosphatase, type II
mm10_v2_chr6_-_129623840_129623866	0.0489792	Msx2_Hoxd4	ENSMUST00000095412.4|Klrk1|ENSMUSG00000030149.9|killer cell lectin-like receptor subfamily K, member 1 	ENSMUST00000168919.1|Klrk1|ENSMUSG00000030149.9|killer cell lectin-like receptor subfamily K, member 1
mm10_v2_chr4_-_82850721_82850814	0.0451311	Msx2_Hoxd4	ENSMUST00000139401.1|Zdhhc21|ENSMUSG00000028403.9|zinc finger, DHHC domain containing 21
mm10_v2_chr7_-_115824699_115824752	0.04309	Msx2_Hoxd4	ENSMUST00000169129.1|Sox6|ENSMUSG00000051910.7|SRY-box containing gene 6
mm10_v2_chr1_+_60908993_60909033	0.0427599	Msx2_Hoxd4	ENSMUST00000027164.2|Ctla4|ENSMUSG00000026011.7|cytotoxic T-lymphocyte-associated protein 4
mm10_v2_chr9_-_107770945_107771007	0.0426692	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_chr17_+_46161021_46161072	0.0418835	Msx2_Hoxd4	ENSMUST00000024748.7|Gtpbp2|ENSMUSG00000023952.7|GTP binding protein 2 	ENSMUST00000172170.1|Gtpbp2|ENSMUSG00000023952.7|GTP binding protein 2
mm10_v2_chr11_+_76904513_76904569	0.0417463	Msx2_Hoxd4	ENSMUST00000072633.3|Tmigd1|ENSMUSG00000020839.10|transmembrane and immunoglobulin domain containing 1
mm10_v2_chr8_-_3625274_3625288	0.0384332	Msx2_Hoxd4	ENSMUST00000004749.6|Pcp2|ENSMUSG00000004630.12|Purkinje cell protein 2 (L7)
mm10_v2_chr4_-_129261394_129261406	0.0380796	Msx2_Hoxd4	ENSMUST00000145261.1|C77080|ENSMUSG00000050390.6|expressed sequence C77080
mm10_v2_chr15_-_37459327_37459380	0.03651	Msx2_Hoxd4	ENSMUST00000119730.1|Ncald|ENSMUSG00000051359.8|neurocalcin delta 	ENSMUST00000120746.1|Ncald|ENSMUSG00000051359.8|neurocalcin delta
mm10_v2_chrX_-_103981242_103981287	0.0362967	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	0.0360661	Msx2_Hoxd4	ENSMUST00000114606.1|Etl4|ENSMUSG00000036617.10|enhancer trap locus 4 	ENSMUST00000114608.1|Etl4|ENSMUSG00000036617.10|enhancer trap locus 4
mm10_v2_chr7_-_45920830_45920883	0.0359523	Msx2_Hoxd4	ENSMUST00000164119.1|Emp3|ENSMUSG00000040212.5|epithelial membrane protein 3
mm10_v2_chr1_-_133661318_133661386	0.035409	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_chr7_+_123123870_123123901	0.0347214	Msx2_Hoxd4	ENSMUST00000094053.5|Tnrc6a|ENSMUSG00000052707.7|trinucleotide repeat containing 6a
mm10_v2_chr2_-_144527341_144527424	0.0328427	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_chr1_-_190170671_190170744	0.0324068	Msx2_Hoxd4	ENSMUST00000175916.1|Prox1|ENSMUSG00000010175.7|prospero-related homeobox 1
mm10_v2_chr10_+_39612934_39612934	0.0317814	Msx2_Hoxd4	ENSMUST00000019987.6|Traf3ip2|ENSMUSG00000019842.6|TRAF3 interacting protein 2
mm10_v2_chrX_-_143933089_143933142	0.0313894	Msx2_Hoxd4	ENSMUST00000087313.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chr18_+_68337504_68337603	0.0311338	Msx2_Hoxd4	ENSMUST00000172148.1|Mc5r|ENSMUSG00000007480.3|melanocortin 5 receptor
mm10_v2_chr3_+_40800778_40800786	0.0309825	Msx2_Hoxd4	ENSMUST00000169566.1|Plk4|ENSMUSG00000025758.5|polo-like kinase 4
mm10_v2_chr1_+_165788746_165788769	0.0309325	Msx2_Hoxd4	ENSMUST00000161559.2|Cd247|ENSMUSG00000005763.9|CD247 antigen
mm10_v2_chr16_-_58524164_58524179	0.0306634	Msx2_Hoxd4	ENSMUST00000126978.1|St3gal6|ENSMUSG00000022747.10|ST3 beta-galactoside alpha-2,3-sialyltransferase 6 	ENSMUST00000123918.1|St3gal6|ENSMUSG00000022747.10|ST3 beta-galactoside alpha-2,3-sialyltransferase 6
mm10_v2_chr2_-_72813665_72813717	0.0305819	Msx2_Hoxd4	ENSMUST00000136807.1|6430710C18Rik|ENSMUSG00000085427.1|RIKEN cDNA 6430710C18 gene 	ENSMUST00000148327.1|6430710C18Rik|ENSMUSG00000085427.1|RIKEN cDNA 6430710C18 gene
mm10_v2_chr2_+_4017727_4017745	0.0299209	Msx2_Hoxd4	ENSMUST00000177457.1|Frmd4a|ENSMUSG00000026657.10|FERM domain containing 4A
mm10_v2_chr18_+_52767994_52768149	0.0288805	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_chr17_-_35046539_35046622	0.0288516	Msx2_Hoxd4	ENSMUST00000007250.7|Msh5|ENSMUSG00000007035.9|mutS homolog 5 (E. coli)
mm10_v2_chr13_+_40859768_40859822	0.0287967	Msx2_Hoxd4	ENSMUST00000110191.2|Gcnt2|ENSMUSG00000021360.9|glucosaminyl (N-acetyl) transferase 2, I-branching enzyme
mm10_v2_chr11_-_99322943_99322957	0.0284053	Msx2_Hoxd4	ENSMUST00000038004.2|Krt25|ENSMUSG00000035831.2|keratin 25
mm10_v2_chr7_+_126950837_126950966	0.028296	Msx2_Hoxd4	ENSMUST00000106332.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2
mm10_v2_chrX_-_8132770_8132857	0.0280984	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_chr2_+_72054598_72054640	0.0276079	Msx2_Hoxd4	ENSMUST00000028525.5|Rapgef4|ENSMUSG00000049044.10|Rap guanine nucleotide exchange factor (GEF) 4
mm10_v2_chr4_+_99272671_99272671	0.0275522	Msx2_Hoxd4	ENSMUST00000094956.1|Gm10305|ENSMUSG00000070892.1|predicted gene 10305
mm10_v2_chr12_-_108179237_108179339	0.0273086	Msx2_Hoxd4	ENSMUST00000071095.7|Setd3|ENSMUSG00000056770.9|SET domain containing 3
mm10_v2_chr18_+_59062462_59062538	0.0268101	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_chrX_-_162964557_162964599	0.0263363	Msx2_Hoxd4	ENSMUST00000038769.2|S100g|ENSMUSG00000040808.4|S100 calcium binding protein G
mm10_v2_chr14_+_14328113_14328113	0.0262258	Msx2_Hoxd4	ENSMUST00000100872.1|Olfr31|ENSMUSG00000072707.1|olfactory receptor 31
mm10_v2_chr9_-_77544829_77544862	0.0262176	Msx2_Hoxd4	ENSMUST00000183734.1|Lrrc1|ENSMUSG00000032352.9|leucine rich repeat containing 1
mm10_v2_chr14_+_53795455_53795455	0.0262066	Msx2_Hoxd4	ENSMUST00000103671.2|B230359F08Rik|ENSMUSG00000087666.2|RIKEN cDNA B230359F08 gene
mm10_v2_chr12_+_52516077_52516077	0.0260554	Msx2_Hoxd4	ENSMUST00000110725.1|Arhgap5|ENSMUSG00000035133.8|Rho GTPase activating protein 5
mm10_v2_chr13_+_75967704_75967753	0.025544	Msx2_Hoxd4	ENSMUST00000022081.1|Spata9|ENSMUSG00000021590.6|spermatogenesis associated 9
mm10_v2_chr13_-_95250166_95250336	0.0249074	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_chr4_+_124657646_124657656	0.0244717	Msx2_Hoxd4	ENSMUST00000053491.7|Pou3f1|ENSMUSG00000090125.2|POU domain, class 3, transcription factor 1
mm10_v2_chr1_-_133921393_133921414	0.0242689	Msx2_Hoxd4	ENSMUST00000048432.5|Prelp|ENSMUSG00000041577.5|proline arginine-rich end leucine-rich repeat
mm10_v2_chr15_-_101786458_101786528	0.023336	Msx2_Hoxd4	ENSMUST00000071104.4|Krt72|ENSMUSG00000056605.6|keratin 72
mm10_v2_chr1_+_171840557_171840570	0.0231608	Msx2_Hoxd4	ENSMUST00000135386.1|Cd84|ENSMUSG00000038147.7|CD84 antigen
mm10_v2_chr12_-_85374696_85374719	0.0228393	Msx2_Hoxd4	ENSMUST00000040766.7|Tmed10|ENSMUSG00000021248.8|transmembrane emp24-like trafficking protein 10 (yeast)
mm10_v2_chr10_-_13324160_13324242	0.0227887	Msx2_Hoxd4	ENSMUST00000105545.4|Phactr2|ENSMUSG00000062866.9|phosphatase and actin regulator 2
mm10_v2_chr3_-_49757257_49757316	0.0223389	Msx2_Hoxd4	ENSMUST00000035931.7|Pcdh18|ENSMUSG00000037892.8|protocadherin 18
mm10_v2_chr4_+_101507947_101508032	0.0218018	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_chr4_-_62519885_62519967	0.0191766	Msx2_Hoxd4	ENSMUST00000107444.1|Alad|ENSMUSG00000028393.4|aminolevulinate, delta-, dehydratase 	ENSMUST00000030090.3|Alad|ENSMUSG00000028393.4|aminolevulinate, delta-, dehydratase
mm10_v2_chr4_-_119492563_119492628	0.018863	Msx2_Hoxd4	ENSMUST00000049994.7|Rimkla|ENSMUSG00000048899.8|ribosomal modification protein rimK-like family member A
mm10_v2_chr5_-_107875035_107875107	0.0184845	Msx2_Hoxd4	ENSMUST00000138111.1|Evi5|ENSMUSG00000011831.10|ecotropic viral integration site 5 	ENSMUST00000112642.1|Evi5|ENSMUSG00000011831.10|ecotropic viral integration site 5
mm10_v2_chr3_+_52268337_52268388	0.0181861	Msx2_Hoxd4	ENSMUST00000053764.5|Foxo1|ENSMUSG00000044167.5|forkhead box O1
mm10_v2_chr5_-_62766153_62766246	0.0181436	Msx2_Hoxd4	ENSMUST00000076623.4|Arap2|ENSMUSG00000037999.9|ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2
mm10_v2_chr6_-_136941887_136941911	0.0175534	Msx2_Hoxd4	ENSMUST00000111891.1|Arhgdib|ENSMUSG00000030220.7|Rho, GDP dissociation inhibitor (GDI) beta
mm10_v2_chr3_+_64081642_64081642	0.0171552	Msx2_Hoxd4	ENSMUST00000029406.4|Vmn2r1|ENSMUSG00000027824.4|vomeronasal 2, receptor 1
mm10_v2_chr4_-_3872105_3872105	0.0166216	Msx2_Hoxd4	ENSMUST00000105158.1|Mos|ENSMUSG00000078365.5|Moloney sarcoma oncogene
mm10_v2_chr1_+_165788681_165788728	0.0164904	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_chr3_-_79145875_79145930	0.0160471	Msx2_Hoxd4	ENSMUST00000118340.1|Rapgef2|ENSMUSG00000062232.8|Rap guanine nucleotide exchange factor (GEF) 2
mm10_v2_chr1_-_153844130_153844158	0.01593	Msx2_Hoxd4	ENSMUST00000124558.3|Rgsl1|ENSMUSG00000042641.12|regulator of G-protein signaling like 1
mm10_v2_chr7_+_65693417_65693446	0.0158467	Msx2_Hoxd4	ENSMUST00000032726.7|Tm2d3|ENSMUSG00000078681.4|TM2 domain containing 3 	ENSMUST00000107495.3|Tm2d3|ENSMUSG00000078681.4|TM2 domain containing 3
mm10_v2_chr7_-_34654342_34654398	0.0156615	Msx2_Hoxd4	ENSMUST00000108069.1|Kctd15|ENSMUSG00000030499.3|potassium channel tetramerisation domain containing 15
mm10_v2_chr12_+_31438209_31438227	0.014799	Msx2_Hoxd4	ENSMUST00000001254.5|Slc26a3|ENSMUSG00000001225.6|solute carrier family 26, member 3
mm10_v2_chr11_+_96292453_96292508	0.0145191	Msx2_Hoxd4	ENSMUST00000173432.1|Hoxb6|ENSMUSG00000000690.4|homeobox B6
mm10_v2_chr2_-_60125651_60125775	0.0143498	Msx2_Hoxd4	ENSMUST00000112550.1|Baz2b|ENSMUSG00000026987.10|bromodomain adjacent to zinc finger domain, 2B
mm10_v2_chr10_+_128303322_128303352	0.0142652	Msx2_Hoxd4	ENSMUST00000005825.6|Pan2|ENSMUSG00000005682.8|PAN2 polyA specific ribonuclease subunit homolog (S. cerevisiae)
mm10_v2_chr15_-_37458523_37458581	0.014091	Msx2_Hoxd4	ENSMUST00000116445.2|Ncald|ENSMUSG00000051359.8|neurocalcin delta
mm10_v2_chr5_-_23616528_23616597	0.0138266	Msx2_Hoxd4	ENSMUST00000088392.4|Srpk2|ENSMUSG00000062604.7|serine/arginine-rich protein specific kinase 2
mm10_v2_chrX_+_136245065_136245102	0.0128312	Msx2_Hoxd4	ENSMUST00000048687.4|Wbp5|ENSMUSG00000042712.4|WW domain binding protein 5
mm10_v2_chr8_-_117082449_117082449	0.0127639	Msx2_Hoxd4	ENSMUST00000098375.4|Pkd1l2|ENSMUSG00000034416.12|polycystic kidney disease 1 like 2 	ENSMUST00000109093.2|Pkd1l2|ENSMUSG00000034416.12|polycystic kidney disease 1 like 2
mm10_v2_chr14_+_54259227_54259241	0.012407	Msx2_Hoxd4	ENSMUST00000041197.7|Abhd4|ENSMUSG00000040997.7|abhydrolase domain containing 4
mm10_v2_chr1_-_172632931_172632974	0.011631	Msx2_Hoxd4	ENSMUST00000027826.5|Dusp23|ENSMUSG00000026544.5|dual specificity phosphatase 23
mm10_v2_chr7_-_84679346_84679401	0.0114038	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_chr15_-_101743099_101743117	0.0109327	Msx2_Hoxd4	ENSMUST00000023710.4|Krt71|ENSMUSG00000051879.3|keratin 71
mm10_v2_chr15_+_82345954_82346035	0.0097363	Msx2_Hoxd4	ENSMUST00000023086.8|Smdt1|ENSMUSG00000022452.8|single-pass membrane protein with aspartate rich tail 1
mm10_v2_chr13_+_21362826_21362883	0.00945148	Msx2_Hoxd4	ENSMUST00000053293.6|Zscan12|ENSMUSG00000036721.7|zinc finger and SCAN domain containing 12
mm10_v2_chr19_+_26749726_26749877	0.00922825	Msx2_Hoxd4	ENSMUST00000175842.1|Smarca2|ENSMUSG00000024921.10|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
mm10_v2_chrX_-_94123359_94123412	0.0079718	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_chr1_+_191025350_191025350	0.0077099	Msx2_Hoxd4	ENSMUST00000181050.1|A230020J21Rik|ENSMUSG00000097845.1|RIKEN cDNA A230020J21 gene
mm10_v2_chr1_-_149961230_149961300	0.00716243	Msx2_Hoxd4	ENSMUST00000070200.8|Pla2g4a|ENSMUSG00000056220.8|phospholipase A2, group IVA (cytosolic, calcium-dependent)
mm10_v2_chr3_+_144570687_144570721	0.00640223	Msx2_Hoxd4	ENSMUST00000106211.1|Sep15|ENSMUSG00000037072.9|selenoprotein
mm10_v2_chr3_+_62419668_62419668	0.00618358	Msx2_Hoxd4	ENSMUST00000161057.1|Arhgef26|ENSMUSG00000036885.8|Rho guanine nucleotide exchange factor (GEF) 26
mm10_v2_chr1_+_60746358_60746427	0.00584019	Msx2_Hoxd4	ENSMUST00000027165.2|Cd28|ENSMUSG00000026012.2|CD28 antigen
mm10_v2_chr1_+_180109192_180109265	0.00550691	Msx2_Hoxd4	ENSMUST00000143176.1|Cdc42bpa|ENSMUSG00000026490.11|CDC42 binding protein kinase alpha 	ENSMUST00000135056.1|Cdc42bpa|ENSMUSG00000026490.11|CDC42 binding protein kinase alpha
mm10_v2_chr1_+_157526127_157526153	0.00448118	Msx2_Hoxd4	ENSMUST00000111700.1|Sec16b|ENSMUSG00000026589.8|SEC16 homolog B (S. cerevisiae)
mm10_v2_chr9_-_77544870_77544914	0.00446465	Msx2_Hoxd4	ENSMUST00000183873.1|Lrrc1|ENSMUSG00000032352.9|leucine rich repeat containing 1
mm10_v2_chr5_-_84417359_84417389	0.00443613	Msx2_Hoxd4	ENSMUST00000113401.1|Epha5|ENSMUSG00000029245.10|Eph receptor A5
mm10_v2_chr2_-_107059646_107059658	0.00402572	Msx2_Hoxd4	ENSMUST00000028533.6|Fshb|ENSMUSG00000027120.6|follicle stimulating hormone beta
mm10_v2_chr19_+_46396885_46397004	0.00382755	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_chr17_-_25785324_25785343	0.00350246	Msx2_Hoxd4	ENSMUST00000150324.1|Haghl|ENSMUSG00000061046.3|hydroxyacylglutathione hydrolase-like
mm10_v2_chr18_+_37320374_37320401	0.003433	Msx2_Hoxd4	ENSMUST00000078271.2|Pcdhb5|ENSMUSG00000063687.2|protocadherin beta 5
mm10_v2_chr18_-_37969742_37969782	0.00338339	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_chr4_+_35152056_35152056	0.00307948	Msx2_Hoxd4	ENSMUST00000058595.6|Ifnk|ENSMUSG00000042993.6|interferon kappa
mm10_v2_chr7_-_101845300_101845339	0.00302706	Msx2_Hoxd4	ENSMUST00000094141.5|Folr2|ENSMUSG00000032725.9|folate receptor 2 (fetal)
mm10_v2_chr10_+_52391606_52391610	0.00302169	Msx2_Hoxd4	ENSMUST00000067085.4|Nepn|ENSMUSG00000038624.11|nephrocan
mm10_v2_chr5_+_65348386_65348406	0.00259523	Msx2_Hoxd4	ENSMUST00000031096.7|Klb|ENSMUSG00000029195.7|klotho beta
mm10_v2_chr2_+_35622010_35622063	0.00243397	Msx2_Hoxd4	ENSMUST00000091010.5|Dab2ip|ENSMUSG00000026883.11|disabled 2 interacting protein
mm10_v2_chr1_-_163289214_163289235	0.00182073	Msx2_Hoxd4	ENSMUST00000183691.1|Prrx1|ENSMUSG00000026586.10|paired related homeobox 1
mm10_v2_chr6_-_87533219_87533264	0.00108372	Msx2_Hoxd4	ENSMUST00000113637.2|Arhgap25|ENSMUSG00000030047.8|Rho GTPase activating protein 25 	ENSMUST00000071024.6|Arhgap25|ENSMUSG00000030047.8|Rho GTPase activating protein 25
mm10_v2_chr13_+_76098734_76098809	0.000493273	Msx2_Hoxd4	ENSMUST00000091466.3|Ttc37|ENSMUSG00000033991.8|tetratricopeptide repeat domain 37
mm10_v2_chr7_+_96522342_96522398	0.000484938	Msx2_Hoxd4	ENSMUST00000129737.1|Tenm4|ENSMUSG00000048078.10|teneurin transmembrane protein 4
mm10_v2_chr4_-_141078302_141078357	0.000323841	Msx2_Hoxd4	ENSMUST00000030760.8|Necap2|ENSMUSG00000028923.8|NECAP endocytosis associated 2
