It's a truth (or at least fan theory) universally acknowledged that Jon Snow and Daenerys Targaryen are going to get together by the end of Game of Thrones. George R.R. Martin's series is called A Song of Ice and Fire after all. But, since the R+L=J theory turned out to be very true, it's also a truth universally acknowledged that Jon and Dany are related. The only part that's not understood is exactly how they're related. But good news: It's not as complicated as it seems. Let's start with the Targaryen family basics.
The Targaryen family tree is a ~whole thing~ but don't worry: You don't need to memorize it—Daenerys' immediate family is all that matters here.
Dany has two brothers: Rhaegar and Viserys. All three were the children of Aerys II, AKA The Mad King. To put all of that into context, The Mad King ruled Westeros before Robert Baratheon. He's the guy Jaime Lannister killed, earning him that lovely nickname "Kingslayer."
Now, let's talk about Dany's brothers. First, there's Viserys (who we met in Season 1), the guy who sold Dany to a rapist in an attempt to raise an army (this endeavor did not end well...as in, he died a gruesome death). More importantly, we have Dany's brother Rhaegar, which brings us to....
How Jon fits in:
This is a good time to remind everyone that R+L=J stands for Rhaegar+Lyanna=Jon. That's right: Dany's brother Rhaegar Targaryen is Jon Snow's real, biological father. So where does that leave us on the issue of just how he and Dany are related?
The short version:
Dany is Jon's aunt. That's it. They're not cousins, they are in no way "removed." She is just straight up his aunt and he's her nephew.
So...can they still end up together?
Yes! In the Game of Thrones world, they totally, definitely can. Targaryens have a long history of marrying siblings (see the chart above) in an attempt to keep their mystical, dragon-infused bloodline pure (if Dany had been older, she probably would have married Rhaegar—wrap your head around that). So by their standards, an aunt and nephew are almost not related enough.