| ACTL6B | actin-like 6B | 21 |
| ACTN2 | actinin, alpha 2 | 40 |
| AEBP1 | AE binding protein 1 | 20 |
| ARNT | aryl hydrocarbon receptor nuclear translocator-like | 10 |
| ARNTL | aryl hydrocarbon receptor nuclear translocator | 1 |
| ASCL1 | achaete-scute complex homolog 1 (Drosophila) | 20 |
| BASP1 | brain abundant, membrane attached signal protein 1 | 30 |
| BCL10 | B-cell CLL/lymphoma 10 | 9 |
| BCL11A | B-cell CLL/lymphoma 11A (zinc finger protein) | 1 |
| BCORL1 | BCL6 corepressor | 10 |
| BRCA1 | breast cancer 1, early onset | 101 |
| CBX4 | chromobox homolog 4 | 29 |
| CCNE1 | cyclin E1 | 10 |
| CDX2 | caudal type homeobox 2 | 10 |
| CITED1 | Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 | 1 |
| CREB1 | cAMP responsive element binding protein 1 | 9 |
| CREBBP | CREB binding protein | 13 |
| CREM | cAMP responsive element modulator | 1 |
| CTBP1 | C-terminal binding protein 1 | 10 |
| CTBP2 | C-terminal binding protein 2 | 1 |
| DCC | deleted in colorectal carcinoma | 192 |
| DNMT3B | DNA (cytosine-5-)-methyltransferase 3 beta | 14 |
| E4F1 | E4F transcription factor 1 | 1 |
| ENO1 | enolase 1, (alpha) | 1 |
| ESRRB | estrogen-related receptor beta | 10 |
| FEV | FEV (ETS oncogene family) | 1 |
| FGF22 | fibroblast growth factor 2 (basic) | 9 |
| FLJ36070 | MEF2 activating motif and SAP domain containing transcriptional regulator | 20 |
| GATA3 | GATA binding protein 3 | 11 |
| GATA4 | GATA binding protein 4 | 21 |
| HAND1 | heart and neural crest derivatives expressed 1 | 54 |
| HAND2 | heart and neural crest derivatives expressed 2 | 30 |
| HCFC1 | host cell factor C1 (VP16-accessory protein) | 9 |
| HDAC1 | histone deacetylase 1 | 13 |
| HDAC4 | histone deacetylase 4 | 1 |
| HEY1 | hairy/enhancer-of-split related with YRPW motif 1 | 9 |
| HEYL | hairy/enhancer-of-split related with YRPW motif-like | 20 |
| HSF4 | heat shock transcription factor 4 | 11 |
| ID4 | inhibitor of DNA binding 4, dominant negative helix-loop-helix protein | 10 |
| IRF3 | interferon regulatory factor 3 | 1 |
| ISL1 | ISL LIM homeobox 1 | 1 |
| JMY | junction mediating and regulatory protein, p53 cofactor | 1 |
| JUB | ajuba LIM protein | 1 |
| JUNB | jun B proto-oncogene | 9 |
| KCNIP3 | Kv channel interacting protein 3, calsenilin | 1 |
| KCTD1 | potassium channel tetramerization domain containing 1 | 29 |
| KDM1 | lysine (K)-specific demethylase 1A | 1 |
| LBXCOR1 | SKI family transcriptional corepressor 1 | 10 |
| LHX1 | LIM homeobox 1 | 95 |
| LHX2 | LIM homeobox 2 | 41 |
