Now that HBO has officially confirmed Rhaegar Targaryen as Jon Snow’s father, the new ‘King in the North’ also has the best claim to become the King of the Seven Kingdoms. Even if Jon turns out to be Rhaegar’s bastard, he is still his only surviving child which gives him a better claim than anyone else alive, even Daenerys (who is now his aunt actually).
This makes things very interesting because Daenerys looks all set to take the Iron Throne from Cersei Lannister very soon, as she was close to King’s Landing in season 6 finale. With Northern Houses declaring Jon Snow as the King in the North, they have also effectively exited from the Seven Kingdoms. This also means that even if Daenerys takes the throne, she will never be a legal ruler of the North, an area believed to be as large as the rest of the Seven Kingdoms.
So, the most likely way for Daenerys to secure the North will be through marriage. This was also heavily implied during her breakup with Daario in season 6 finale. Therefore, if Daenerys does marry Jon Snow, it is likely that she will still be the main ruler because Jon anyways lacks the desire to rule at present. This can however change if both become aware of Jon’s true parentage and Daenerys decides to voluntarily step down.
This brings us to another big question- How will they come to know of this huge game changing information? The people who currently have access to this information are Bran Stark and Howland Reed (and most likely the handmaidens inside the Tower of Joy). Ideally, Bran should be the one to tell Jon about this but that would be too convenient for a show like Game of Thrones. He was left near The Wall by Benjen Stark and there is currently no way of telling how his storyline will pan out in season 7. He has the Night King’s mark on his hand and that should not be a good news for the people of Westeros, once he gets south of The Wall.
Some fans believe that Littlefinger might also be aware of Jon’s true parentage. This was also hinted in season 5 when he was in the crypts of Winterfell with Sansa. He also made it pretty clear in season 6 that he does not like Jon Snow and wants the Iron Throne for himself with Sansa by his side. So even if Lord Baelish knows about Jon’s parentage, it is unlikely that he will ever reveal this secret. In fact, he might even try to suppress this information from ever coming out.
We all know that claims mean nothing in Game of Thrones and as Cersei showed in season 6 finale, only the powerful and the cunning survive in the world of ice and fire. Jon Snow might be a skilled fighter and an amazing person at heart but he presently lacks the desire and the head to be the King of the Seven Kingdoms. Whether or not this will change, only time will tell.