Well, l have got the same question several days ago.My Bible teacher told me that "where are you from"rerfers to the country you lived in,while second one do not mean that,it refers to the situation you may travel or do bussiness from one place to another,someone ask you the place you come from.

(2) Where do you come from?

Good question! They mean the same.

hello my dear how are you doing, i am contact is because i like you love is between two people please i will like you to contact my contact so i will tell you more about me because i am not come online is why i need you, favourme10@hotmail. com

While they both mean the same thing, "Where are you from" is more informal and relaxed. This is the expression/question we would ask in the United States.