If memory serves, he was given the tatoo of XIII by Hojo. Branding his test subjects with numbers was a common practice of his and it's very demeaning to do to intelligent beings.

Of his family, we clearly can see that Seto is of the same species. Presumably, his mother was also of the same species, although she's not mentioned by name even seen in flashbacks. Bugenhagen takes on the role of wise mentor to Nanaki, so it'd be natural for him to refer to him affectionately as grandfather.