To reduce power draw, I recommend you do all 4 of these:
Follow the various sections in [url]Jetson/Performance - eLinux.org to reduce the CPU speed of the 4 cores to be as low as possible for your application.
Also, if you don’t need anything displayed on a screen then make sure nothing is plugged into your HDMI port, and possibly also disable it, see [url]Jetson/Jetson TK1 Power - eLinux.org.
And if you won’t be running intense code for long periods, then try tp replaeing the fan with a heatsink, see [url]Jetson/Thermal - eLinux.org.
As you already knew that fan is controlled by pin PMU_REGEN3, and that pin also controls some other power.
So there’s no simple way to just cut down fan power.