Game of Thrones: How Are Daenerys and Jon Related?

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Finally, after many seasons of speculation, Game of Thrones has confirmed R + L = J. Jon Snow is the son of Lyanna Stark and (presumably) Rhaegar Targaryen, making him Ned Stark's nephew, not his son. This is a tragedy on many different levels - the first and most obvious being that Jon Snow and Daenerys Targaryen are related, so if they end up married, it'll be icky. Rhaegar Targaryen is Daenerys's oldest brother, making Jon Snow her nephew and therefore heir presumptive to the Targaryen throne. On the other hand, incest is still very prevalent among Westerosi royals and the Targaryens, so it could still happen, though we wholeheartedly hope not . . .