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Kobo's Aura HD does popup footnotes too. It also has a larger, 6.8 inch high definition screen and uses the kePub format mentioned in fjTorres's post above. It's lighter than the Kindle Fire HDX which is worth considering if you do much reading. You don't mention how large your library of ePub books is, but it's worth noting that the Aura HD has a copy of the Adobe rendering engine in addition to the more advanced ACCESS engine so you can read ePubs straight out of ADE.
Calibre has plugins to reformat your ePubs into either AZW3 or kePub formats but it only works with files that have no DRM. One more thing to consider.
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