Each cell has the same DNA. As this is the case there must be ways for cells to differentiate from other cells while all cells have the same DNA. In different cell types different genes are translated which is achieved by genes in different cell types having different epigenetic marks. Epigenetic marks on genes can increase or decrease transcription of genes. DNA methylation and histone methylation are two ways genes can be epigenetically marked and thereby transcription of genes affected. There are various other ways that genes can be epigenetically marked. Environment can affect what epigenetic marks are on genes.
With genetic diseases there is systematic evidence of genetic anomalies. Take any cell from the body and genes in that cell will show the genetic anomaly. For example, blood tests can be used to detect genetic anomalies With epigenetic diseases, however, there is no genetic evidence of the disease and dysregulations do not have to be systematic whereby bloods tests might not be revealing.
Vitamin D is now suspected to play a part in lots of illnesses and I think this is correct but with epigenetic anomalies there need not be any genetic anomalies though there is still disease. The last step in the formation of calcitriol, which is active vitamin D, by CYP27B1 requires an iron-sulfur protein called adrenodoxin. Due to difficulties in forming iron-sulfur clusters there will be low levels of adrenodoxin whereby there are low levels of calcitriol. Giving calcitriol alone, however, is not sufficient to treat many illnesses where there is evidence of calcitriol deficiencies. With iron-sulfur proteins dysregulated a lot of processes besides the formation of calcitriol will also be adversely affected.
There not being diseases associated with aberrant epigenetic marks is basically impossible given the large part that epigenetics plays in regulations of cells. I think schizophrenia is an illness associated with epigenetic dysgulations, an illness in which there are deficiencies of vitamin D but which is basically non-responsive to calcitriol.