I've met men named Jan (pronounced "YAHN") and women named Jan ("JAN"), so I don't really have a strong tendency to assume that the person is either male or female. It depends on what the name is paired with. If it's paired with a Scandinavian or German surname, I wonder if the person is male, but if the last name is something like Miller or Smith, I'm more inclined to think that the person is probably female.
I don't really care for it either way to be honest. I think it would be refreshing to meet a little girl named Jan, but I don't have a very good association with the name, so I wouldn't use it myself. Jan ("YAHN") reminds me of the word "yawn", so I wouldn't want to use it for a boy either.