Hey no not exactly, you would probably not use them interchangeably. "You have nothing on me" you as slang.
A. Hey check out my be dance move!
B. haha "you have nothing in me"
Now "you have nothing over me" you would use if say, someone threatens to say something about you or whatever. You would say "you have nothing over me". As to say your threats are empty.
Well I hope this helps you, I don't know if I was very clear but this were the best examples I could come up with.