#2 is the more standard form, but most speakers would consider either acceptable.
In the first, 'what' is essentially treated as a substitute for 'which', which may function either as subject or as complement, allowing us, for instance, to point at a person in a photograph and ask either
Which (one) are you?
('You' as subject and 'which' as complement)
Which (one) is you?
('which' as subject and 'you' as complement)
with no appreciable difference of meaning.