First, "What is and What are" is typically used for non-living things or ideas. So avoid using "What are you" to a person. The only context in which, perhaps it is used is in the same sense as "What is your occupation"
e.g. What are you ? A doctor or an engineer ?
A better way to convey the same meaning as "What are you" is by asking "What qualities do you have", "What are you like", "What do you look like" etc.
"What are you" is very frequently used when it is followed by some other words like :
What are You looking for ?
What are you doing today ?
What are you talking about ?
"What's your job" will mean what the occupation of the other person is. This meaning hold in most of the contexts. It can also be used when you meet a person somewhere and you think he shouldn't be there. You can ask him "What's your job here?" (not very frequently used)