“Where are you” is the correct structure when you are asking a direct question. When asking a direct question you always change the order of the subject and the main verb.
“…..where you are” could also be correct if the question is an indirect question. An indirect question has some additional words before “where you are” and is a way to be more polite in English.
Where are you going?
Would it be possible for you to tell me where you are going?
Notice that both examples have the same intention but the second example adds extra information.
Where are you?
“Where are you?” is correct when it comes at the beginning of the sentence.
Where are you taking the children?
Where are you going after work?
Where are you parking the car?
Where you are?
“Where you are” is correct when it forms part of an indirect sentence.
Do you know where you are going?
Can you tell me where you are bringing that basket?
Do you mind telling me where you are going with that tennis racket?