You don't even need a motherboard as the fan controller just plugs into the power supply. Only very few fan controllers have any interaction with the motherboard and in all these cases it is optional, eg. Bitfenix Recon's USN internet enabled feature.
Usually fan controllers only connect to the PSU, the only cable that connects to the MB is the one that show the CPU's fan RPM (if you are using it to control the CPU fan)
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