where = 哪里 (nǎli) ,the third tone one is for making a question: where is XXX?
over there = 那里(nàli),the forth tone is for answering the above question(where is XXX?) like: right over there.
there is a little bit diference between those two caracters.but one is for question(哪里nǎli ) , and the other(那里nàli) is for the answer.
do u know the meaning of the caracter “口”? in chinese, it means "mouth". so , can you imagine that why we use ’哪里‘ for making a question instead of ’那里‘?
the caracter 有 just have one tone (the third tone) in chinese.