If you're White, "where are you from" means "where are you from". However, if you're not White (namely, if you're Asian or have a vague ethnicity) it's the way that people who are ignorant about the correct way to talk about race ask about your ethnicity.
The standard example conversation:
"Where are you from?"
"Oregon, born and raised."
"No, I mean, where are you
really from?"
"... Oregon? Oh. You mean... Ah. My mother is from Taiwan, my father is White."
"What's your first language?"
"..."
The other common but incorrect way to ask about race is "What's your nationality", as that's just not what the word means.
Anyway,
@SciTech Outline, I'd say just respond with an approximation of your actual geographic location. In the very least, it might subtly show people that the question doesn't actually ask what they're trying to ask. If people are directly asking about your ethnicity, do what you feel comfortable with, but keep in mind that it probably is just curiosity about you and not inherently offensive. There's a difference between "racial" and "racist", and it's fine to say "I actually am unsure about my ethnic background!" People being curious about you ain't a bad thing, it's only a problem if they're trying to be like "omg of course the tech guy is indian lol outsourcing lol".