mm10_v2_chr5_-_62766153_62766246	5.57117	Msx2_Hoxd4	ENSMUST00000076623.4|Arap2|ENSMUSG00000037999.9|ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2
mm10_v2_chr15_+_21111452_21111452	4.4157	Msx2_Hoxd4	ENSMUST00000075132.6|Cdh12|ENSMUSG00000040452.8|cadherin 12
mm10_v2_chr1_+_159737510_159737510	3.53845	Msx2_Hoxd4	ENSMUST00000111669.3|Tnr|ENSMUSG00000015829.8|tenascin R
mm10_v2_chr2_+_4017727_4017745	3.19926	Msx2_Hoxd4	ENSMUST00000177457.1|Frmd4a|ENSMUSG00000026657.10|FERM domain containing 4A
mm10_v2_chr2_-_63184253_63184292	2.37885	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_+_62419668_62419668	2.12192	Msx2_Hoxd4	ENSMUST00000161057.1|Arhgef26|ENSMUSG00000036885.8|Rho guanine nucleotide exchange factor (GEF) 26
mm10_v2_chr14_-_88471396_88471396	1.87872	Msx2_Hoxd4	ENSMUST00000061628.5|Pcdh20|ENSMUSG00000050505.6|protocadherin 20
mm10_v2_chr6_-_136171722_136171849	1.8523	Msx2_Hoxd4	ENSMUST00000053880.6|Grin2b|ENSMUSG00000030209.8|glutamate receptor, ionotropic, NMDA2B (epsilon 2)
mm10_v2_chr5_-_62765618_62765656	1.81649	Msx2_Hoxd4	ENSMUST00000159470.1|Arap2|ENSMUSG00000037999.9|ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2
mm10_v2_chr12_+_74297474_74297474	1.80934	Msx2_Hoxd4	ENSMUST00000072100.3|Dbpht2|ENSMUSG00000029878.5|DNA binding protein with his-thr domain
mm10_v2_chrX_+_101640056_101640108	1.6987	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_chr15_+_92597104_92597121	1.56809	Msx2_Hoxd4	ENSMUST00000035399.8|Pdzrn4|ENSMUSG00000036218.9|PDZ domain containing RING finger 4
mm10_v2_chr7_-_73537621_73537766	1.55802	Msx2_Hoxd4	ENSMUST00000172704.1|Chd2|ENSMUSG00000078671.4|chromodomain helicase DNA binding protein 2
mm10_v2_chr1_+_165788681_165788728	1.54398	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_-_85741389_85741389	1.44923	Msx2_Hoxd4	ENSMUST00000094148.4|Fam160a1|ENSMUSG00000051000.11|family with sequence similarity 160, member A1
mm10_v2_chr1_-_163725123_163725232	1.41065	Msx2_Hoxd4	ENSMUST00000159679.1|Mettl11b|ENSMUSG00000040113.8|methyltransferase like 11B
mm10_v2_chr11_+_103133303_103133332	1.38243	Msx2_Hoxd4	ENSMUST00000107037.1|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2
mm10_v2_chr10_+_39612934_39612934	1.3267	Msx2_Hoxd4	ENSMUST00000019987.6|Traf3ip2|ENSMUSG00000019842.6|TRAF3 interacting protein 2
mm10_v2_chr1_+_165788746_165788769	1.31709	Msx2_Hoxd4	ENSMUST00000161559.2|Cd247|ENSMUSG00000005763.9|CD247 antigen
mm10_v2_chr3_-_146495115_146495139	1.282	Msx2_Hoxd4	ENSMUST00000093951.2|Spata1|ENSMUSG00000028188.7|spermatogenesis associated 1
mm10_v2_chr2_-_63184170_63184195	1.26659	Msx2_Hoxd4	ENSMUST00000112452.1|Kcnh7|ENSMUSG00000059742.4|potassium voltage-gated channel, subfamily H (eag-related), member 7
mm10_v2_chr3_-_66296807_66296837	1.24071	Msx2_Hoxd4	ENSMUST00000029419.7|Veph1|ENSMUSG00000027831.9|ventricular zone expressed PH domain-containing 1
mm10_v2_chr7_+_126950518_126950584	1.18275	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_chr11_+_103133333_103133359	1.17681	Msx2_Hoxd4	ENSMUST00000124928.1|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2 	ENSMUST00000062530.4|Hexim2|ENSMUSG00000043372.6|hexamethylene bis-acetamide inducible 2
mm10_v2_chr2_-_144527341_144527424	1.16986	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_chrX_-_143933089_143933142	1.14046	Msx2_Hoxd4	ENSMUST00000087313.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chr18_+_37513652_37513652	1.13444	Msx2_Hoxd4	ENSMUST00000061405.4|Pcdhb21|ENSMUSG00000044022.4|protocadherin beta 21
mm10_v2_chr4_-_129121889_129122063	1.10393	Msx2_Hoxd4	ENSMUST00000139450.1|Hpca|ENSMUSG00000028785.6|hippocalcin 	ENSMUST00000125931.1|Hpca|ENSMUSG00000028785.6|hippocalcin 	ENSMUST00000116444.2|Hpca|ENSMUSG00000028785.6|hippocalcin
mm10_v2_chr1_+_180109192_180109265	1.08614	Msx2_Hoxd4	ENSMUST00000143176.1|Cdc42bpa|ENSMUSG00000026490.11|CDC42 binding protein kinase alpha 	ENSMUST00000135056.1|Cdc42bpa|ENSMUSG00000026490.11|CDC42 binding protein kinase alpha
mm10_v2_chr7_+_96522342_96522398	1.00495	Msx2_Hoxd4	ENSMUST00000129737.1|Tenm4|ENSMUSG00000048078.10|teneurin transmembrane protein 4
mm10_v2_chr17_-_90088343_90088373	0.957283	Msx2_Hoxd4	ENSMUST00000173917.1|Nrxn1|ENSMUSG00000024109.12|neurexin I
mm10_v2_chr6_-_36811361_36811361	0.952367	Msx2_Hoxd4	ENSMUST00000101534.1|Ptn|ENSMUSG00000029838.8|pleiotrophin
mm10_v2_chr17_-_46327949_46327987	0.950208	Msx2_Hoxd4	ENSMUST00000047970.7|Abcc10|ENSMUSG00000032842.7|ATP-binding cassette, sub-family C (CFTR/MRP), member 10
mm10_v2_chr1_-_152625212_152625220	0.929746	Msx2_Hoxd4	ENSMUST00000027760.7|Rgl1|ENSMUSG00000026482.7|ral guanine nucleotide dissociation stimulator,-like 1
mm10_v2_chr17_-_25785324_25785343	0.90615	Msx2_Hoxd4	ENSMUST00000150324.1|Haghl|ENSMUSG00000061046.3|hydroxyacylglutathione hydrolase-like
mm10_v2_chr9_-_55919605_55919605	0.901311	Msx2_Hoxd4	ENSMUST00000037408.8|Scaper|ENSMUSG00000034007.9|S phase cyclin A-associated protein in the ER
mm10_v2_chr18_-_37969742_37969782	0.892497	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_chr9_-_112187766_112187862	0.884001	Msx2_Hoxd4	ENSMUST00000111872.2|Arpp21|ENSMUSG00000032503.11|cyclic AMP-regulated phosphoprotein, 21 	ENSMUST00000164754.2|Arpp21|ENSMUSG00000032503.11|cyclic AMP-regulated phosphoprotein, 21
mm10_v2_chr14_-_36919314_36919352	0.875816	Msx2_Hoxd4	ENSMUST00000182797.1|Ccser2|ENSMUSG00000058690.8|coiled-coil serine rich 2
mm10_v2_chr1_+_72284367_72284419	0.874597	Msx2_Hoxd4	ENSMUST00000027380.5|Tmem169|ENSMUSG00000026188.5|transmembrane protein 169 	ENSMUST00000141783.1|Tmem169|ENSMUSG00000026188.5|transmembrane protein 169
mm10_v2_chr4_+_124657646_124657656	0.866714	Msx2_Hoxd4	ENSMUST00000053491.7|Pou3f1|ENSMUSG00000090125.2|POU domain, class 3, transcription factor 1
mm10_v2_chrX_+_56454871_56454887	0.861824	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_chrX_+_159708593_159708612	0.847141	Msx2_Hoxd4	ENSMUST00000080394.6|Sh3kbp1|ENSMUSG00000040990.11|SH3-domain kinase binding protein 1
mm10_v2_chr8_-_120228221_120228297	0.840299	Msx2_Hoxd4	ENSMUST00000183235.1|A330074K22Rik|ENSMUSG00000097960.1|RIKEN cDNA A330074K22 gene
mm10_v2_chr1_+_33908172_33908225	0.837128	Msx2_Hoxd4	ENSMUST00000182513.1|Dst|ENSMUSG00000026131.11|dystonin 	ENSMUST00000183034.1|Dst|ENSMUSG00000026131.11|dystonin
mm10_v2_chr2_-_72986716_72986716	0.8345	Msx2_Hoxd4	ENSMUST00000112062.1|Gm11084|ENSMUSG00000079286.1|predicted gene 11084
mm10_v2_chr6_+_136518820_136518851	0.813553	Msx2_Hoxd4	ENSMUST00000032335.6|Atf7ip|ENSMUSG00000030213.6|activating transcription factor 7 interacting protein
mm10_v2_chr4_+_102570065_102570124	0.806995	Msx2_Hoxd4	ENSMUST00000097950.2|Pde4b|ENSMUSG00000028525.10|phosphodiesterase 4B, cAMP specific
mm10_v2_chr5_-_84417359_84417389	0.784605	Msx2_Hoxd4	ENSMUST00000113401.1|Epha5|ENSMUSG00000029245.10|Eph receptor A5
mm10_v2_chr2_-_45112890_45113010	0.776278	Msx2_Hoxd4	ENSMUST00000076836.6|Zeb2|ENSMUSG00000026872.10|zinc finger E-box binding homeobox 2
mm10_v2_chr2_-_33086366_33086447	0.750073	Msx2_Hoxd4	ENSMUST00000049618.2|Garnl3|ENSMUSG00000038860.9|GTPase activating RANGAP domain-like 3
mm10_v2_chr7_-_73541738_73541758	0.742856	Msx2_Hoxd4	ENSMUST00000169922.2|Chd2|ENSMUSG00000078671.4|chromodomain helicase DNA binding protein 2
mm10_v2_chr2_-_45110336_45110487	0.742015	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_chr16_+_14705832_14705858	0.736747	Msx2_Hoxd4	ENSMUST00000023356.6|Snai2|ENSMUSG00000022676.6|snail homolog 2 (Drosophila)
mm10_v2_chrX_-_8132770_8132857	0.732025	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_chr7_+_126950687_126950729	0.724712	Msx2_Hoxd4	ENSMUST00000106333.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2
mm10_v2_chr5_-_146220901_146220987	0.724635	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_chr18_+_52767994_52768149	0.717521	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_chr4_-_40722307_40722398	0.671455	Msx2_Hoxd4	ENSMUST00000181475.1|Gm6297|ENSMUSG00000097123.1|predicted gene 6297
mm10_v2_chrX_-_143933204_143933311	0.661055	Msx2_Hoxd4	ENSMUST00000112851.1|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000112856.2|Dcx|ENSMUSG00000031285.8|doublecortin 	ENSMUST00000033642.3|Dcx|ENSMUSG00000031285.8|doublecortin
mm10_v2_chr3_+_138065052_138065078	0.660824	Msx2_Hoxd4	ENSMUST00000163080.2|1110002E22Rik|ENSMUSG00000090066.2|RIKEN cDNA 1110002E22 gene
mm10_v2_chr5_-_107875035_107875107	0.652353	Msx2_Hoxd4	ENSMUST00000138111.1|Evi5|ENSMUSG00000011831.10|ecotropic viral integration site 5 	ENSMUST00000112642.1|Evi5|ENSMUSG00000011831.10|ecotropic viral integration site 5
mm10_v2_chr15_-_37459327_37459380	0.645592	Msx2_Hoxd4	ENSMUST00000119730.1|Ncald|ENSMUSG00000051359.8|neurocalcin delta 	ENSMUST00000120746.1|Ncald|ENSMUSG00000051359.8|neurocalcin delta
mm10_v2_chr7_-_121074501_121074530	0.639892	Msx2_Hoxd4	ENSMUST00000047194.2|Igsf6|ENSMUSG00000035004.2|immunoglobulin superfamily, member 6
mm10_v2_chr13_+_76098734_76098809	0.62464	Msx2_Hoxd4	ENSMUST00000091466.3|Ttc37|ENSMUSG00000033991.8|tetratricopeptide repeat domain 37
mm10_v2_chr3_-_110143937_110144011	0.621311	Msx2_Hoxd4	ENSMUST00000051253.3|Ntng1|ENSMUSG00000050836.3|netrin G1
mm10_v2_chr7_+_126950837_126950966	0.587278	Msx2_Hoxd4	ENSMUST00000106332.1|Sez6l2|ENSMUSG00000030683.5|seizure related 6 homolog like 2
mm10_v2_chr9_+_32116040_32116136	0.546435	Msx2_Hoxd4	ENSMUST00000174641.1|Arhgap32|ENSMUSG00000041444.8|Rho GTPase activating protein 32
mm10_v2_chr9_-_50739365_50739517	0.540182	Msx2_Hoxd4	ENSMUST00000117093.1|Dixdc1|ENSMUSG00000032064.11|DIX domain containing 1 	ENSMUST00000121634.1|Dixdc1|ENSMUSG00000032064.11|DIX domain containing 1
mm10_v2_chrX_+_150547375_150547459	0.53991	Msx2_Hoxd4	ENSMUST00000066337.6|Alas2|ENSMUSG00000025270.7|aminolevulinic acid synthase 2, erythroid 	ENSMUST00000112715.1|Alas2|ENSMUSG00000025270.7|aminolevulinic acid synthase 2, erythroid
mm10_v2_chr19_+_26749726_26749877	0.533588	Msx2_Hoxd4	ENSMUST00000175842.1|Smarca2|ENSMUSG00000024921.10|SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
mm10_v2_chr2_-_176144697_176144697	0.525323	Msx2_Hoxd4	ENSMUST00000178872.1|Gm2004|ENSMUSG00000095648.1|predicted gene 2004
mm10_v2_chrX_-_94123359_94123412	0.511674	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_chr4_-_141078302_141078357	0.502648	Msx2_Hoxd4	ENSMUST00000030760.8|Necap2|ENSMUSG00000028923.8|NECAP endocytosis associated 2
mm10_v2_chr7_+_123123870_123123901	0.472634	Msx2_Hoxd4	ENSMUST00000094053.5|Tnrc6a|ENSMUSG00000052707.7|trinucleotide repeat containing 6a
mm10_v2_chr2_-_60125651_60125775	0.47056	Msx2_Hoxd4	ENSMUST00000112550.1|Baz2b|ENSMUSG00000026987.10|bromodomain adjacent to zinc finger domain, 2B
mm10_v2_chr13_+_51408618_51408781	0.470408	Msx2_Hoxd4	ENSMUST00000087978.3|S1pr3|ENSMUSG00000067586.3|sphingosine-1-phosphate receptor 3
mm10_v2_chr18_+_37320374_37320401	0.468981	Msx2_Hoxd4	ENSMUST00000078271.2|Pcdhb5|ENSMUSG00000063687.2|protocadherin beta 5
mm10_v2_chr18_+_37518341_37518359	0.459276	Msx2_Hoxd4	ENSMUST00000097609.1|Pcdhb22|ENSMUSG00000073591.3|protocadherin beta 22
mm10_v2_chr11_-_87826023_87826113	0.457604	Msx2_Hoxd4	ENSMUST00000103177.3|Lpo|ENSMUSG00000009356.6|lactoperoxidase
mm10_v2_chr11_+_95010277_95010293	0.425073	Msx2_Hoxd4	ENSMUST00000124735.1|Samd14|ENSMUSG00000047181.6|sterile alpha motif domain containing 14
mm10_v2_chr3_-_49757257_49757316	0.416186	Msx2_Hoxd4	ENSMUST00000035931.7|Pcdh18|ENSMUSG00000037892.8|protocadherin 18
mm10_v2_chr15_-_79285502_79285537	0.407616	Msx2_Hoxd4	ENSMUST00000165408.1|Baiap2l2|ENSMUSG00000018126.9|BAI1-associated protein 2-like 2
mm10_v2_chr3_+_68869563_68869589	0.403895	Msx2_Hoxd4	ENSMUST00000054551.2|1110032F04Rik|ENSMUSG00000046999.2|RIKEN cDNA 1110032F04 gene
mm10_v2_chr5_-_23616528_23616597	0.40094	Msx2_Hoxd4	ENSMUST00000088392.4|Srpk2|ENSMUSG00000062604.7|serine/arginine-rich protein specific kinase 2
mm10_v2_chr15_-_37458523_37458581	0.398074	Msx2_Hoxd4	ENSMUST00000116445.2|Ncald|ENSMUSG00000051359.8|neurocalcin delta
mm10_v2_chr1_-_133661318_133661386	0.38823	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_-_29906524_29906572	0.374406	Msx2_Hoxd4	ENSMUST00000159920.1|Zfp27|ENSMUSG00000062040.8|zinc finger protein 27 	ENSMUST00000162592.1|Zfp27|ENSMUSG00000062040.8|zinc finger protein 27
mm10_v2_chr1_-_190170178_190170237	0.363094	Msx2_Hoxd4	ENSMUST00000177288.1|Prox1|ENSMUSG00000010175.7|prospero-related homeobox 1
mm10_v2_chr9_-_107770945_107771007	0.345913	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_chr16_-_44016387_44016436	0.316533	Msx2_Hoxd4	ENSMUST00000036174.3|Gramd1c|ENSMUSG00000036292.7|GRAM domain containing 1C
mm10_v2_chrM_+_9870_9885	0.316374	Msx2_Hoxd4	ENSMUST00000084013.1|mt-Nd4l|ENSMUSG00000065947.3|mitochondrially encoded NADH dehydrogenase 4L
mm10_v2_chr18_+_59062462_59062538	0.288529	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_chr13_+_75967704_75967753	0.282534	Msx2_Hoxd4	ENSMUST00000022081.1|Spata9|ENSMUSG00000021590.6|spermatogenesis associated 9
mm10_v2_chr12_+_36314160_36314171	0.281247	Msx2_Hoxd4	ENSMUST00000041407.5|Sostdc1|ENSMUSG00000036169.5|sclerostin domain containing 1
mm10_v2_chr1_-_24612700_24612700	0.277636	Msx2_Hoxd4	ENSMUST00000088336.1|Gm10222|ENSMUSG00000067736.1|predicted gene 10222
mm10_v2_chr11_-_109472611_109472688	0.276644	Msx2_Hoxd4	ENSMUST00000168740.1|Slc16a6|ENSMUSG00000041920.8|solute carrier family 16 (monocarboxylic acid transporters), member 6
mm10_v2_chr1_+_157458554_157458597	0.274089	Msx2_Hoxd4	ENSMUST00000046743.4|BC026585|ENSMUSG00000033488.5|cDNA sequence BC026585 	ENSMUST00000119891.1|BC026585|ENSMUSG00000033488.5|cDNA sequence BC026585
mm10_v2_chr18_-_3281712_3281747	0.263659	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_chr1_+_137928100_137928170	0.251477	Msx2_Hoxd4	ENSMUST00000054333.2|A130050O07Rik|ENSMUSG00000051480.2|RIKEN cDNA A130050O07 gene
mm10_v2_chr17_+_46161021_46161072	0.248206	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	0.246571	Msx2_Hoxd4	ENSMUST00000020016.4|Gje1|ENSMUSG00000019867.4|gap junction protein, epsilon 1
mm10_v2_chr10_+_75037066_75037100	0.238115	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_-_106800051_106800095	0.237952	Msx2_Hoxd4	ENSMUST00000013882.7|Crbn|ENSMUSG00000005362.8|cereblon 	ENSMUST00000049675.4|Crbn|ENSMUSG00000005362.8|cereblon 	ENSMUST00000113239.3|Crbn|ENSMUSG00000005362.8|cereblon
mm10_v2_chr4_-_149126688_149126763	0.230332	Msx2_Hoxd4	ENSMUST00000030815.2|Cort|ENSMUSG00000028971.4|cortistatin
mm10_v2_chr10_+_128303322_128303352	0.228811	Msx2_Hoxd4	ENSMUST00000005825.6|Pan2|ENSMUSG00000005682.8|PAN2 polyA specific ribonuclease subunit homolog (S. cerevisiae)
mm10_v2_chr18_+_34840575_34840589	0.215446	Msx2_Hoxd4	ENSMUST00000043484.7|Reep2|ENSMUSG00000038555.7|receptor accessory protein 2
mm10_v2_chr8_-_70527645_70527783	0.210387	Msx2_Hoxd4	ENSMUST00000132867.1|Kxd1|ENSMUSG00000055553.10|KxDL motif containing 1
mm10_v2_chr13_+_93304799_93304935	0.20358	Msx2_Hoxd4	ENSMUST00000080127.5|Homer1|ENSMUSG00000007617.11|homer homolog 1 (Drosophila)
mm10_v2_chr18_+_23752333_23752401	0.196607	Msx2_Hoxd4	ENSMUST00000170802.1|Mapre2|ENSMUSG00000024277.8|microtubule-associated protein, RP/EB family, member 2 	ENSMUST00000155708.1|Mapre2|ENSMUSG00000024277.8|microtubule-associated protein, RP/EB family, member 2 	ENSMUST00000118826.2|Mapre2|ENSMUSG00000024277.8|microtubule-associated protein, RP/EB family, member 2
mm10_v2_chr1_-_132390301_132390373	0.196181	Msx2_Hoxd4	ENSMUST00000132435.1|Tmcc2|ENSMUSG00000042066.9|transmembrane and coiled-coil domains 2
mm10_v2_chr6_+_37870786_37870882	0.194635	Msx2_Hoxd4	ENSMUST00000120428.1|Trim24|ENSMUSG00000029833.11|tripartite motif-containing 24 	ENSMUST00000031859.7|Trim24|ENSMUSG00000029833.11|tripartite motif-containing 24
mm10_v2_chrX_-_103981242_103981287	0.165043	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_chr13_-_75943812_75943950	0.164272	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_chrX_-_74246534_74246556	0.15438	Msx2_Hoxd4	ENSMUST00000101454.2|Flna|ENSMUSG00000031328.9|filamin, alpha 	ENSMUST00000033699.6|Flna|ENSMUSG00000031328.9|filamin, alpha
mm10_v2_chr13_-_95250166_95250336	0.149267	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_chr14_+_54259227_54259241	0.145957	Msx2_Hoxd4	ENSMUST00000041197.7|Abhd4|ENSMUSG00000040997.7|abhydrolase domain containing 4
mm10_v2_chr6_+_34746368_34746393	0.145522	Msx2_Hoxd4	ENSMUST00000142716.1|Cald1|ENSMUSG00000029761.10|caldesmon 1
mm10_v2_chr18_-_43477764_43477836	0.132607	Msx2_Hoxd4	ENSMUST00000057110.9|Eif3j2|ENSMUSG00000043424.9|eukaryotic translation initiation factor 3, subunit J2
mm10_v2_chr13_+_93304066_93304138	0.123839	Msx2_Hoxd4	ENSMUST00000109493.1|Homer1|ENSMUSG00000007617.11|homer homolog 1 (Drosophila)
mm10_v2_chr6_+_124304646_124304671	0.111291	Msx2_Hoxd4	ENSMUST00000112541.2|Cd163|ENSMUSG00000008845.3|CD163 antigen 	ENSMUST00000032234.2|Cd163|ENSMUSG00000008845.3|CD163 antigen
mm10_v2_chr6_+_15196949_15197102	0.104776	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_-_74724670_74724702	0.102495	Msx2_Hoxd4	ENSMUST00000021091.8|Pafah1b1|ENSMUSG00000020745.9|platelet-activating factor acetylhydrolase, isoform 1b, subunit 1
mm10_v2_chr4_-_119492563_119492628	0.095435	Msx2_Hoxd4	ENSMUST00000049994.7|Rimkla|ENSMUSG00000048899.8|ribosomal modification protein rimK-like family member A
mm10_v2_chr15_-_50890396_50890463	0.0874387	Msx2_Hoxd4	ENSMUST00000185183.1|Trps1|ENSMUSG00000038679.10|trichorhinophalangeal syndrome I (human)
mm10_v2_chr12_-_27160311_27160476	0.0844663	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_chr9_+_30942541_30942562	0.0803223	Msx2_Hoxd4	ENSMUST00000068135.6|Adamts8|ENSMUSG00000031994.7|a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 8
mm10_v2_chr10_+_127421124_127421203	0.0735493	Msx2_Hoxd4	ENSMUST00000170336.1|R3hdm2|ENSMUSG00000025404.9|R3H domain containing 2
mm10_v2_chr19_-_53371766_53371766	0.0734749	Msx2_Hoxd4	ENSMUST00000086887.1|Gm10197|ENSMUSG00000067085.1|predicted gene 10197
mm10_v2_chr6_+_34745952_34746007	0.0708589	Msx2_Hoxd4	ENSMUST00000123823.1|Cald1|ENSMUSG00000029761.10|caldesmon 1 	ENSMUST00000136907.1|Cald1|ENSMUSG00000029761.10|caldesmon 1 	ENSMUST00000126181.1|Cald1|ENSMUSG00000029761.10|caldesmon 1
mm10_v2_chr12_-_76177251_76177265	0.0635734	Msx2_Hoxd4	ENSMUST00000101291.3|Esr2|ENSMUSG00000021055.7|estrogen receptor 2 (beta) 	ENSMUST00000076634.4|Esr2|ENSMUSG00000021055.7|estrogen receptor 2 (beta)
mm10_v2_chr8_-_8639363_8639363	0.0521038	Msx2_Hoxd4	ENSMUST00000152698.1|Efnb2|ENSMUSG00000001300.9|ephrin B2
mm10_v2_chr5_-_31179901_31179942	0.0498067	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_chr2_+_72054598_72054640	0.0440901	Msx2_Hoxd4	ENSMUST00000028525.5|Rapgef4|ENSMUSG00000049044.10|Rap guanine nucleotide exchange factor (GEF) 4
mm10_v2_chr2_+_109280738_109280798	0.0344651	Msx2_Hoxd4	ENSMUST00000028527.7|Kif18a|ENSMUSG00000027115.8|kinesin family member 18A
mm10_v2_chr12_+_52516077_52516077	0.027877	Msx2_Hoxd4	ENSMUST00000110725.1|Arhgap5|ENSMUSG00000035133.8|Rho GTPase activating protein 5
mm10_v2_chr19_+_46396885_46397004	0.0275946	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_chr4_-_148160031_148160083	0.0269887	Msx2_Hoxd4	ENSMUST00000057907.3|Fbxo44|ENSMUSG00000029001.9|F-box protein 44
mm10_v2_chr10_+_127421208_127421235	0.0256154	Msx2_Hoxd4	ENSMUST00000168780.1|R3hdm2|ENSMUSG00000025404.9|R3H domain containing 2
mm10_v2_chr1_+_191025350_191025350	0.0230249	Msx2_Hoxd4	ENSMUST00000181050.1|A230020J21Rik|ENSMUSG00000097845.1|RIKEN cDNA A230020J21 gene
mm10_v2_chrX_-_150814265_150814345	0.0222789	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_chrM_+_10167_10167	0.0210189	Msx2_Hoxd4	ENSMUST00000082414.1|mt-Nd4|ENSMUSG00000064363.1|mitochondrially encoded NADH dehydrogenase 4
mm10_v2_chr4_-_148159838_148159930	0.0170178	Msx2_Hoxd4	ENSMUST00000151127.1|Fbxo44|ENSMUSG00000029001.9|F-box protein 44 	ENSMUST00000105705.2|Fbxo44|ENSMUSG00000029001.9|F-box protein 44
mm10_v2_chr4_+_136143497_136143497	0.00924421	Msx2_Hoxd4	ENSMUST00000008016.2|Id3|ENSMUSG00000007872.3|inhibitor of DNA binding 3
mm10_v2_chr3_+_84952146_84952186	0.00690347	Msx2_Hoxd4	ENSMUST00000029727.7|Fbxw7|ENSMUSG00000028086.8|F-box and WD-40 domain protein 7
mm10_v2_chr6_+_29361410_29361461	0.00551021	Msx2_Hoxd4	ENSMUST00000156163.1|Calu|ENSMUSG00000029767.10|calumenin
