| HOXA7 | homeobox A7 | 7p15.2
| 10.861 |
| HOXA9 | homeobox A9 | 7p15.2
| 10.597 |
| HOXA6 | homeobox A6 | 7p15.2
| 10.522 |
| HOXA-AS3 | HOXA cluster antisense RNA 3 | 7p15.2
| 10.495 |
| HOXA4 | homeobox A4 | 7p15.2
| 10.448 |
| HOXA5 | homeobox A5 | 7p15.2
| 10.437 |
| HOXA10-AS | HOXA10 antisense RNA | 7p15.2
| 10.31 |
| HOXA3 | homeobox A3 | 7p15.2
| 10.292 |
| MIR196B | microRNA 196b | 7p15.2
| 10.266 |
| HOXD11 | homeobox D11 | 2q31.1
| 10.117 |
| HOXA-AS2 | HOXA cluster antisense RNA 2 | 7p15.2
| 10.052 |
| HOXD10 | homeobox D10 | 2q31.1
| 10.012 |
| HOXA10 | homeobox A10 | 7p15.2
| 9.901 |
| HOXD9 | homeobox D9 | 2q31.1
| 9.644 |
| HOXA10-HOXA9 | NA | NA
| 9.484 |
| HOXA11 | homeobox A11 | 7p15.2
| 9.368 |
| HOXD12 | homeobox D12 | 2q31.1
| 9.361 |
| HOXA11-AS | HOXA11 antisense RNA | 7p15.2
| 9.357 |
| HOXD8 | homeobox D8 | 2q31.1
| 9.26 |
| HOXB-AS3 | HOXB cluster antisense RNA 3 | 17q21.32
| 9.114 |
| HOXB5 | homeobox B5 | 17q21.32
| 9.083 |
| HOXB3 | homeobox B3 | 17q21.32
| 8.973 |
| HOXB4 | homeobox B4 | 17q21.32
| 8.945 |
| HOXB6 | homeobox B6 | 17q21.32
| 8.929 |
| MIR10A | microRNA 10a | 17q21.32
| 8.924 |
| HOXB7 | homeobox B7 | 17q21.32
| 8.855 |
| HOXA2 | homeobox A2 | 7p15.2
| 8.792 |
| HOXA13 | homeobox A13 | 7p15.2
| 8.747 |
| HOTTIP | HOXA distal transcript antisense RNA | 7p15.2
| 8.717 |
| HOXB8 | homeobox B8 | 17q21.32
| 8.662 |
| HOXD13 | homeobox D13 | 2q31.1
| 8.614 |
| HOXD-AS2 | HOXD cluster antisense RNA 2 | 2q31.1
| 8.601 |
| NR2F1 | nuclear receptor subfamily 2, group F, member 1 | 5q14
| 8.26 |
| NR2F1-AS1 | NR2F1 antisense RNA 1 | 5q15
| 8.173 |
| MIR10B | microRNA 10b | 2q31.1
| 8.007 |
| HOXD4 | homeobox D4 | 2q31.1
| 7.95 |
| HOXB9 | homeobox B9 | 17q21.32
| 7.783 |
| EVX2 | even-skipped homeobox 2 | 2q31.1
| 7.748 |
| HOTAIRM1 | HOXA transcript antisense RNA, myeloid-specific 1 | 7p15.2
| 7.654 |
| HOXA1 | homeobox A1 | 7p15.2
| 7.631 |
| HOXC-AS2 | HOXC cluster antisense RNA 2 | 12q13.13
| 7.564 |
| HOXC-AS1 | HOXC cluster antisense RNA 1 | 12q13.13
| 7.472 |
| HOXC9 | homeobox C9 | 12q13.13
| 7.47 |
| MIR196A2 | microRNA 196a-2 | 12q13.13
| 7.279 |
| DLX6 | distal-less homeobox 6 | 7q21.3
| 7.237 |
| HOXC8 | homeobox C8 | 12q13.13
| 7.236 |
| MIR196A1 | microRNA 196a-1 | 17q21.32
| 7.211 |
| LINC00461 | long intergenic non-protein coding RNA 461 | 5q14.3
| 7.197 |
| HOXC6 | homeobox C6 | 12q13.13
| 7.068 |
| HOXC4 | homeobox C4 | 12q13.13
| 7.047 |
| HOXC5 | homeobox C5 | 12q13.13
| 7.047 |
| HOXC-AS3 | HOXC cluster antisense RNA 3 | 12q13.13
| 6.992 |
| HOXC10 | homeobox C10 | 12q13.13
| 6.974 |
| MIR615 | microRNA 615 | 12q13.13
| 6.956 |
| DLX6-AS1 | DLX6 antisense RNA 1 | 7q21.3
| 6.824 |
| TFAP2A-AS1 | TFAP2A antisense RNA 1 | 6p24.3
| 6.819 |
| TFAP2A | transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha) | 6p24.3
| 6.814 |
| MIR9-2 | microRNA 9-2 | 5q14.3
| 6.768 |
| HOXB2 | homeobox B2 | 17q21.32
| 6.714 |
| NR2F2 | nuclear receptor subfamily 2, group F, member 2 | 15q26
| 6.697 |
| HOXD3 | homeobox D3 | 2q31.1
| 6.696 |
| MIR1469 | microRNA 1469 | 15q26.2
| 6.692 |
| HOTAIR | HOX transcript antisense RNA | 12q13.13
| 6.668 |
| HOXB-AS1 | HOXB cluster antisense RNA 1 | 17q21.32
| 6.66 |
| KAZALD1 | Kazal-type serine peptidase inhibitor domain 1 | 10q24.32
| 6.634 |
| HOXC11 | homeobox C11 | 12q13.13
| 6.613 |
| CBX8 | chromobox homolog 8 | 17q25.3
| 6.429 |
| PAX3 | paired box 3 | 2q36.1
| 6.391 |
| CCDC140 | coiled-coil domain containing 140 | 2q36.1
| 6.359 |
| HOXC12 | homeobox C12 | 12q13.13
| 6.255 |
| LBX1 | ladybird homeobox 1 | 10q24.32
| 6.247 |
| LBX1-AS1 | LBX1 antisense RNA 1 (head to head) | 10q24.32
| 6.191 |
| CDX2 | caudal type homeobox 2 | 13q12.2
| 6.107 |
| SP9 | Sp9 transcription factor | 2q31.1
| 6.086 |
| ZIC4 | Zic family member 4 | 3q24
| 6.02 |
| POU3F3 | POU class 3 homeobox 3 | 2q12.1
| 6.013 |
| GATA4 | GATA binding protein 4 | 8p23.1-p22
| 5.984 |
| PRDM12 | PR domain containing 12 | 9q34.12
| 5.893 |
| NR2F2-AS1 | NR2F2 antisense RNA 1 | 15q26.2
| 5.853 |
| POU3F2 | POU class 3 homeobox 2 | 6q16.2
| 5.846 |
| ZIC1 | Zic family member 1 | 3q24
| 5.838 |
| LHX2 | LIM homeobox 2 | 9q33.3
| 5.802 |
| HAND2 | heart and neural crest derivatives expressed 2 | 4q34.1
| 5.718 |
| HAND2-AS1 | HAND2 antisense RNA 1 (head to head) | 4q34.1
| 5.703 |
| ONECUT1 | one cut homeobox 1 | 15q21.3
| 5.643 |
| DLX5 | distal-less homeobox 5 | 7q21.3
| 5.628 |
| EVX1 | even-skipped homeobox 1 | 7p15.2
| 5.576 |
| LINC01158 | long intergenic non-protein coding RNA 1158 | 2q12.1
| 5.567 |
| PDX1-AS1 | PDX1 antisense RNA 1 | 13q12.2
| 5.451 |
| WNT10A | wingless-type MMTV integration site family, member 10A | 2q35
| 5.446 |
| PDX1 | pancreatic and duodenal homeobox 1 | 13q12.1
| 5.398 |
| MIR2277 | microRNA 2277 | 5
| 5.351 |
| EVX1-AS | EVX1 antisense RNA | 7p15.2
| 5.327 |
| HAGLR | HOXD antisense growth-associated long non-coding RNA | 2q31.1
| 5.324 |
| HAGLROS | HAGLR opposite strand (non-protein coding) | 2q31.1
| 5.321 |
| SHOX | short stature homeobox | Xp22.33 and Yp11.32
| 5.32 |
| PAX6 | paired box 6 | 11p13
| 5.312 |
| LINC01305 | long intergenic non-protein coding RNA 1305 | 2q31.1
| 5.308 |
| VAX2 | ventral anterior homeobox 2 | 2p13.3
| 5.274 |
| PAX2 | paired box 2 | 10q24.31
| 5.212 |
| CDKN2A | cyclin-dependent kinase inhibitor 2A | 9p21
| 5.209 |
| MEIS2 | Meis homeobox 2 | 15q14
| 5.199 |
| CDKN2B-AS1 | CDKN2B antisense RNA 1 | 9p21.3
| 5.189 |
| PAX7 | paired box 7 | 1p36.13
| 5.185 |
| MT1JP | metallothionein 1J, pseudogene | 16q12.2
| 5.183 |
| POU4F3 | POU class 4 homeobox 3 | 5q32
| 5.176 |
| LINC01410 | long intergenic non-protein coding RNA 1410 | 9q13
| 5.162 |
| WNT7B | wingless-type MMTV integration site family, member 7B | 22q13
| 5.162 |
| LHX9 | LIM homeobox 9 | 1q31.1
| 5.161 |
| MT1A | metallothionein 1A | 16q13
| 5.152 |
| MT1M | metallothionein 1M | 16q13
| 5.139 |
| EMX2OS | EMX2 opposite strand/antisense RNA | 10q26.11
| 5.115 |
| FLJ12825 | NA | NA
| 5.111 |
| DKFZp686K1684 | NA | NA
| 5.093 |
| EMX2 | empty spiracles homeobox 2 | 10q26.11
| 5.061 |
| PAX9 | paired box 9 | 14q13.3
| 5.053 |
| MT1DP | metallothionein 1D, pseudogene (functional) | 16q13
| 5.044 |
| LINC01551 | long intergenic non-protein coding RNA 1551 | 14q11.2
| 5.043 |
| NKX2-3 | NK2 homeobox 3 | 10q24.2
| 5.01 |
| C17orf82 | chromosome 17 open reading frame 82 | 17q23.2
| 5.008 |
| LINC01475 | long intergenic non-protein coding RNA 1475 | 10q24.2
| 5.002 |
| CDKN2A-AS1 | CDKN2A antisense RNA 1 (head to head) | 9p21.3
| 4.989 |
| TBX2 | T-box 2 | 17q23.2
| 4.984 |
| EN1 | engrailed homeobox 1 | 2q14.2
| 4.98 |
| TBX2-AS1 | TBX2 antisense RNA 1 | 17q23.2
| 4.978 |
| MT1E | metallothionein 1E | 16q13
| 4.957 |
| PTF1A | pancreas specific transcription factor, 1a | 10p12.31
| 4.944 |
| LOC648987 | NA | NA
| 4.936 |
| HOXC13-AS | HOXC13 antisense RNA | 12q13.13
| 4.922 |
| EBF2 | early B-cell factor 2 | 8p21.1
| 4.894 |
| LOC440982 | NA | NA
| 4.888 |
| FOXG1 | forkhead box G1 | 14q12
| 4.865 |
| HOXB1 | homeobox B1 | 17q21.32
| 4.863 |
| HAND1 | heart and neural crest derivatives expressed 1 | 5q33
| 4.855 |
| TWIST1 | twist family bHLH transcription factor 1 | 7p21
| 4.843 |
| HOXC13 | homeobox C13 | 12q13.13
| 4.828 |
| WNT6 | wingless-type MMTV integration site family, member 6 | 2q35
| 4.803 |
| HOXB13 | homeobox B13 | 17q21.32
| 4.795 |
| SIM1 | single-minded family bHLH transcription factor 1 | 6q16.3
| 4.784 |
| FOXC1 | forkhead box C1 | 6p25
| 4.77 |
| RUNX2 | runt-related transcription factor 2 | 6p21
| 4.764 |
| PRRX1 | paired related homeobox 1 | 1q24.3
| 4.756 |
| MT1L | metallothionein 1L (gene/pseudogene) | 16q13
| 4.753 |
| MT1B | metallothionein 1B | 16q13
| 4.734 |
| FOXD1 | forkhead box D1 | 5q13.2
| 4.732 |
| FOXG1-AS1 | FOXG1 antisense RNA 1 (head to head) | 14q12
| 4.711 |
| GSX1 | GS homeobox 1 | 13q12.2
| 4.691 |
| ATP5EP2 | ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit pseudogene 2 | 13q12
| 4.69 |
| PRDM8 | PR domain containing 8 | 4q21
| 4.678 |
| MT1F | metallothionein 1F | 16q13
| 4.676 |
| TLX1 | T-cell leukemia homeobox 1 | 10q24.32
| 4.675 |
| TLX1NB | TLX1 neighbor | 10q24
| 4.664 |
| LINC01159 | long intergenic non-protein coding RNA 1159 | 2q12.1
| 4.61 |
| MIR9-3 | microRNA 9-3 | 15q26.1
| 4.608 |
| LMX1B | LIM homeobox transcription factor 1, beta | 9q33.3
| 4.606 |
| CBX4 | chromobox homolog 4 | 17q25.3
| 4.604 |
| MIR3185 | microRNA 3185 | 17
| 4.601 |
| BARHL2 | BarH-like homeobox 2 | 1p22.2
| 4.589 |
| VAX1 | ventral anterior homeobox 1 | 10q26.11
| 4.565 |
| SIM2 | single-minded family bHLH transcription factor 2 | 21q22.2
| 4.559 |
| SATB2 | SATB homeobox 2 | 2q33.1
| 4.547 |
| PRAC2 | prostate cancer susceptibility candidate 2 | 17q21.3
| 4.543 |
| LINC01391 | long intergenic non-protein coding RNA 1391 | 3q22.3
| 4.542 |
| LINC00925 | NA | NA
| 4.526 |
| ZFHX3 | zinc finger homeobox 3 | 16q22.3
| 4.515 |
| FLJ32255 | NA | NA
| 4.511 |
| SATB2-AS1 | SATB2 antisense RNA 1 | 2q33.1
| 4.503 |
| TBX15 | T-box 15 | 1p11.1
| 4.497 |
| BMI1 | BMI1 proto-oncogene, polycomb ring finger | 10p13
| 4.492 |
| FOXCUT | FOXC1 upstream transcript (non-protein coding) | 6p25.3
| 4.471 |
| OTP | orthopedia homeobox | 5q14.1
| 4.451 |
| MT1G | metallothionein 1G | 16q13
| 4.449 |
| PITX2 | paired-like homeodomain 2 | 4q25
| 4.444 |
| POU4F1 | POU class 4 homeobox 1 | 13q31.1
| 4.437 |
| PRAC1 | prostate cancer susceptibility candidate 1 | 17q21
| 4.414 |
| LOC101929234 | NA | NA
| 4.412 |
| EBF3 | early B-cell factor 3 | 10q26.3
| 4.409 |
| LINC01143 | long intergenic non-protein coding RNA 1143 | 2p13.3
| 4.407 |
| PAUPAR | PAX6 upstream antisense RNA | 11p13
| 4.404 |
| ANKRD53 | ankyrin repeat domain 53 | 2p13.3
| 4.392 |
| MT1H | metallothionein 1H | 16q13
| 4.37 |
| SOX1 | SRY (sex determining region Y)-box 1 | 13q34
| 4.369 |
| ZNF503-AS2 | ZNF503 antisense RNA 2 | 10q22.3
| 4.365 |
| PRDM13 | PR domain containing 13 | 6q16.2
| 4.35 |
| ATP6V1B1-AS1 | ATP6V1B1 antisense RNA 1 | 2p13.3
| 4.328 |
| FOXL2 | forkhead box L2 | 3q23
| 4.321 |
| NKX2-6 | NK2 homeobox 6 | 8p21.2
| 4.321 |
| FOXL2NB | FOXL2 neighbor | 3q22.3
| 4.31 |
| SIX3 | SIX homeobox 3 | 2p21
| 4.301 |
| SIX3-AS1 | SIX3 antisense RNA 1 | 2p21
| 4.299 |
| UNCX | UNC homeobox | 7p22.3
| 4.28 |
| MSX1 | msh homeobox 1 | 4p16.2
| 4.272 |
| FBXL16 | F-box and leucine-rich repeat protein 16 | 16p13.3
| 4.249 |
| PTGER4P2-CDK2AP2P2 | PTGER4P2-CDK2AP2P2 readthrough transcribed pseudogene | 9q13
| 4.246 |
| ZNF503 | zinc finger protein 503 | 10q22.3
| 4.236 |
| ASCL1 | achaete-scute family bHLH transcription factor 1 | 12q22-q23
| 4.233 |
| NR2E1 | nuclear receptor subfamily 2, group E, member 1 | 6q21
| 4.22 |
| HSF4 | heat shock transcription factor 4 | 16q21
| 4.215 |
| BARX1 | BARX homeobox 1 | 9q22.32
| 4.208 |
| C1orf53 | chromosome 1 open reading frame 53 | 1q31.3
| 4.204 |