Table 1.

Rewired cRE-promoter interactions in pathogenic gene expression control

Disease	Type of enhancer usage	Variant type	Cause	Result	Reference
Limb malformation	Enhancer-hijacking	Inversion, duplication, deletion	TAD fusion by variants at CTCF-associated boundary domain	Overexpression of WNT or 6IHH or PAX3	47
T cell acute lymphoblastic leukemia	Enhancer-hijacking	Deletion	TAD fusion by variants at CTCF-associated boundary domain	Activation of LMO2 proto-oncogene	50
Medulloblastoma	Enhancer-hijacking	Tandem duplication, deletion, inversion, complex rearrangement	Relocating oncogene proximal to super-enhancer	Activation of GFI1 and GFI1B proto-oncogenes, and overexpression of PRDM6	52, 51
Oncogene activation	Enhancer-hijacking	Tandem duplication	neo-TAD appearance	Overexpression of IGF2	55
Neuroblastoma	Enhancer-hijacking	Copy number alterations	Relocating oncogene proximal to super-enhancer	Overexpression of TERT	53, 54
Branchiooculofacial syndrome	Enhancer disconnection	Inversion	TAD shuffling	Monoallelic and reduced TFAP2A expression	56
Acute myeloid leukemia	Enhancer-hijacking	Inversion	TAD shuffling	Activation of EVI1 proto-oncogene	49