Welcome Newcomer!
A Chassis Fan {CHA_FAN} is for any other fan within the case except the CPU's fan. {e.g. the you connect the rear exhaust fan plug into the Chassis Fan to power the fan} Depending upon your BIOS the CHA_FAN 1-x {Fan} can be speed controlled via the BIOS.
Hope that answers your question. As always, refer to you Manual for more details.