The problem is that even amongst Japanese people (hence there is no conscious racial motive), it's not where you live, but where you were born, or rather where your family register is, that is important. So even if you live in a certain place for many years, you won't be accepted until your family lives there for many generations! There's nothing much to be done about this in Japanese, but when teaching English it's important to let students know that "Where are you from?" doesn't mean, "Where are you born?"; appearance and skin colour don't matter, the answer is where the person themselves feel they come from. Any answer is OK, be it Yorkshire or Imabari!
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Herman Miller|Herman Miller Chairs