Is there a database or study where Quran ayahs are cross referenced? (I would be very surprised if not, as that be an infinitely useful way to study and understand Quran.)

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    There are tafiseer books where the author primarily tries to explain a verse by an other. – Medi1Saif Nov 1 '17 at 16:54

I think there is no such a thing like softwares or databases and interested people can go through Tafseer books.

Tafseer Al-Mizan authored by Allamah Muhammad Hussein Tabatabai is one of most notable of them.

But some books, named Kashf-u-al-ayat (کشف الآیات) (discovering the verses), can be used for this purpose. In fact, they have indices that you can find verses from roots of words.

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