Since the sentence is a question, we need to turn it into a statement to find the subject easily. " So the subject is "differences" and the interrogative pronoun "what" stands for those things that are the differences. If the differences were color and size, as I suggested in the statement, then those would be called the subject complement, or perhaps predicate nominatives.
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Cogarwhat about
What do you think the differences between A and B are ?
If you ask me