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While the word chan is of Japanese origin, chan is not used as a fandom term/genre marker in Japan and almost never seen as a genre marker in Western animanga fandom. Its use in Western media fandom is unlike its use and meaning in Japanese, where it is an affectionate title attached to names, particularly applied to young children and girls. 
Its use in Western media fandom originated in Star Wars fandom, specifically among Qui-Gon/Obi-Wan slashers, who took to calling young Obi-Wan "Obi-chan". Fics about Qui-Gon and underage!Obi-Wan were then called chan.
These stories were controversial because at the time it was unusual for slash fiction to describe characters under the age of eighteen in sexual relationships. There were exceptions, for example A Swedish Bedtime Story from 1997. In this Mulder/Krycek AU Krycek is the fifteen-year-old son of a fisherman. However, the disclaimer implies that the age of the character was perceived as problematic, because it explicitly states that this is not pedophilia and points out that fifteen is the age of consent in Sweden. By the time Qui-Gon/Obi-Wan fanfic conquered slash fandom, the situation had changed to some degree. Inspired by the Jedi Apprentice books where a thirteen year old Obi-Wan is expected to travel the galaxy on his own and take up adult responsibilities, it was argued that if he is old enough to fight and old enough to have a job, he should be old enough to explore his own sexuality.
In February 2000 the chanslash mailing list was founded. This was in part a reaction to a panel at Escapade, where some people argued that Obi-Wan and Qui-Gon had to wait until after Obi-Wan was knighted or it would harm Obi-Wan. Fueled by the conviction that there is no single magic moment like the 18th birthday, or having a braid cut off, that turns a relationship from being harmful to one that isn't, the list was supposed to be a place where stories about a younger Obi-Wan and his interest in his master could be shared and discussed without having to worry about offending other fans who felt these stories were inappropriate.
Although the title description said "Chanslash. A slash only list devoted to the relationship between an older and younger fan fic character", the list was from the very beginning a multifandom list open to any pairing with a teenage character, including same-age pairings. Today "chan" usually refers to fic where one half of the pairing is underage and the other is an adult, although it is sometimes also used for stories pairing two underage characters.
The list manager defined chanslash for the purposes of the list as follows:
- The only requirement I see for any fiction here is that it deal with a slash relationship of fan fic characters at least one of whom is underaged, but NOT pre-puberty, at the beginning of the story. Beyond that any category of story goes. Yes, even elves if you must.
Other sites that archived TPM content used variations of that definition, for example "Chan (teen/adult or teen/teen relationships) is accepted, as long as the younger character(s) shows secondary sexual characteristics" and Master & Apprentice, the main archive for Star Wars: The Phantom Menace slash, still defines chan as age 15-17.
Due to fannish drift the meaning of the term changed when it began to be used in Harry Potter fandom, first including pairings where one character was pre-puberty and then sometimes being limited to pairings where one character was pre-puberty, becoming synonymous with shota. A reason for this might be that sexually explicit fanfiction with characters between 15 and 17 was already common in Harry Potter fandom, and fans may not have seen those stories as needing to be marked by a special term.
Today, because the term chan has so many different meanings, it often needs additional qualifiers to be understood.
- Wikipedia, Japanese honorifics, (Accessed 5 October 2008)
- Anna S. A Swedish Bedtime Story, 1997, (Accessed 10 October 2008)
- Chanslash. Message 1, posted 10 February 2000. Chanslash was a closed list and it doesn't exist anymore. Privately saved email, accessed 10 October 2008.
- Submissions - The Mainframe, 2002. (Accessed 13 January 2011)
- Master & Apprentice Submission Guidelines,(Accessed 10 October 2008)