"Where are you from" is more common (at least in U.S. English).
In my opinion, this is the preferred option when meeting someone new.
The difference is a bit more emphasis on the verb "to be/are" instead of the action of "coming/being from" somewhere as is common in other languages. The meaning is identical though.
1) "Where are you from?" implies that you want to know what city/state/country they consider "home," and that you assume it's someplace other than where you are right now. This may be confusing, since where someone is "from" isn't necessarily where they live. It also can be embarrassing to assume, for example, that a person of a certain ethnic background must "come from" some other place. It might be a good idea to separate the idea of "what is your family/ethnic background?" from "where do you live right now?"
"Where are you from?"
"I'm originally from Oslo, Norway, but I live in Chicago."
2)
"Where do you come from" sounds kind of awkward and outdated. I think this is because it includes the present-tense verb "do" in a question about a past-tense action (coming from somewhere). This is perfectly understandable and you can say this if you prefer - I'd still suggest the other way though.
"Where do you come from?"
"I come from a land beyond the sea, overrun by trolls and dragons!"
3) "Where did you come from" would be correct if you want to know "where were you immediately before you came to this location we're at right now?" This can also be used to express surprise at the person's sudden arrival or unexpected actions.
"Where did you come from?"
"I was next door, but now I'm here to rescue you!"
The interrogative form of verbs in the present simple is formed with DO, not BE. "Where do you come from?" is therefore correct; "Where are you come from?" is not correct.
When BE is functioning as a main verb, DO is not used as an auxiliary for the interrogative: "Where are you from?"
When BE (or any other verb) is functioning as an auxiliary, the interrogative is formed by subject-verb inversion: "Where are you coming from?"
Best Answer
It depends on the question we are answering. Number 1 would be correct in the usual case, when someone asks, "Where are you from?" In that case, we would reply, "I'm from Iran," for example. However, if the person asked us, "Where did you come from?" it may be more natural to answer, "I come from Iran."