In "Eastwatch" (*Game of Thrones*, S07E05), in the scene with Gilly and Sam, Gilly is reading from the records of High Septon Maynard. From this scene, we can infer that this High Septon performed an annulment for Rhaegar Targaryen and married him in secret. I think that it is safe to assume that it was to Lyanna Stark. 

From earlier episodes, we know that this was the coupling that produced Jon Snow. Now, given that they were married and that Rhaegar was the eldest of the siblings, does this make Jon the actual heir over Daenerys?