I think this should be "A szék itt van."
The current word order suggests "this is the correct place for the chair," as opposed to "there is a chair here," which is the meaning I think we're trying to convey.
It means that the CHAIR is here, and not something else. A szék itt van is neutral.
If you mean that the word order is strange, then it's probably because the chair is emphasized, as in: "It is the chair that is here"