So this potlock is a couple of steps away from pure epi, but the theory does rest upon epigenetic markers and is probably one of my favorite theories--(do those exist?)
THIS is Badcock and Crespi's theory of the role parental conflict in fetal development and its role in susceptibility for autism-psychosis spectrum disorders (as well as Angelman's vs Prader-Willi). The epigenetic part of this is that the chromosome is epigenetically marked for different expression in the father and the mother. Therefore, CNV of the same gene can have different results based upon whether this variation is on the maternally inherited or paternally inherited chromosome. Badcock and Crespi showed that this mechanism might account for some of the differences in susceptibility for autism or psychosis spectrum disorders. When a paternally inherited gene is more expressed, the fetus is more likely to develop autism. If the maternally inherited gene is more expressed, the fetus is more likely to have psychosis.