"The Joker does not appear to have any connections to Gotham's crime syndicates, though he knocked over a mob bank. One possible motive for this, which could also explain the clown motif, is the Haley Brothers Circus. The circus was recently in town for a two-month engagement and it was rumored their boss had connections to Sal Maroni. The Joker could be a former Haley Brothers employee with some kind of grudge against the mob."
From that bit of information IGN has put two and two together and it makes quite a bit of sense.
Comics readers will know that Haly's Circus was the home to the Flying Graysons, who were killed after Sal Maroni's associate Tony Zucco sabotaged their ropes in order to send a message to the circus owners that the mob intended on using their trucks to ship drugs. (SPOILER: Speculation that Joseph Gordon-Levitt's cop character John Blake is a potential Batman successor/would-be Robin will only be fueled by the revelation in The Dark Knight Manual that Blake, like Bruce Wayne, is an orphan who "channeled his anger and pain ... into his work serving and protecting the people of Gotham.")
The GCPD report offers one other theory about the Joker's identity: "Given the Joker's access to, and relative comfort with, military-grade technology such as grapple cannons, weaponized gases, explosives, and automatic weapons, it is possible that the man is a former soldier, perhaps suffering from severe PTSD." The report later suggests "anarchy" as a possible motive for Joker's crimes, speculating: "The Joker has murdered or attempted to murder various civic officials. It is possible that he is an extremist anti-government agitator or a soldier angry with the government for sending him to war."