Is there a difference between sleeping late and waking up late vs sleeping early and waking up early?
There is a popular theory that each person has a certain "chronotype" [Ref 1]. Based on your genetics, you could be naturally an early person ("Lark") or a late person ("Owl") [Ref. 2].  What will negatively affect your health is actually fighting what you naturally are.  You probably know which chronotype you are, and if not you can go by what time you naturally sleep/wake when you don't have school/job scheduling such as at the weekend.

[Ref. 1]:Chronotype Review
[Ref. 2]:Social jetlag paper