[Happy Monkey]

Everything else. Everything in a zygote cell is from the sperm or the egg, and it all self-replicates. DNA creates the protein building blocks, but there is all sorts of cellular machinery that uses them to make more cells. Any of it could be affected by a drug or other stimulus. Most of those [disruptive to cell reproduction] effects would probably kill the cell, and most of the rest would probably resume normal operation in the absence of the stimulus, but some could permanently change the operation.

I have a vague memory of a somewhat recent story about prions (or something similar) that did this. Prions can change the output of DNA without affecting the DNA, by changing the way proteins fold.