Upvote:7
It is a rather common source of misunderstanding in ex-Soviet Union countries. Soviet Union used to state your ethnicity in your passport, and in Russian language it is called "национальность" (natsionalnost). It is a second most typical confusion in ex-USSR immigrant/visa communities after "what should I put into Middle Name field"?
When the English language site asks for your nationality, they are asking for your citizenship (гражданство), and not национальность (etnicity). Thus you put Estonian as your nationality.