What are these internal IO connectors for?

Zic

Respectable
Dec 21, 2016
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1,810
1 x AAFP connector
1 x CPU Fan connector(s) (4 -pin)
1 x CPU OPT Fan connector(s) (4 -pin)
6 x Chassis Fan connector(s) (4 -pin)
2 x Assistant Fan connector(s) (1 x 3 -pin, 1 x 4 -pin, [White])
1 x S/PDIF out header(s)
1 x System panel(s) (Q-Connector)
1 x 5-pin EXT_FAN(Extension Fan) connector
1 x Chassis Intrusion connector(s)
3 x Thermal sensor connector(s)
1 x CPU OV
1 x Clear CMOS jumper(s)
1 x Water Pump header (4-pin)

My motherboard is the
https://www.asus.com/us/Motherboards/SABERTOOTH-Z170-S/specifications/
 
Solution
I'm going to go down the line of what you listed them

Front Audio
Umm CPU Fan power!?
Extra CPU Fan power
Extra fans for inside the case power
More Fan power
Optical out "(Had a red glow to it on the back)
All the Power/Light connetors
More Fan power
Switch to let you know if someone has opened the case at all (most cases do NOT have this if bought from a store. More OEM's Pro serioes (Dell Optiplex, HP Eltie have them)
Headers for addon Thermal Sensors
This I am not sure.
Clean the CMOS
If you have a water cooler looks like it has a dedicated header for water coolers
I'm going to go down the line of what you listed them

Front Audio
Umm CPU Fan power!?
Extra CPU Fan power
Extra fans for inside the case power
More Fan power
Optical out "(Had a red glow to it on the back)
All the Power/Light connetors
More Fan power
Switch to let you know if someone has opened the case at all (most cases do NOT have this if bought from a store. More OEM's Pro serioes (Dell Optiplex, HP Eltie have them)
Headers for addon Thermal Sensors
This I am not sure.
Clean the CMOS
If you have a water cooler looks like it has a dedicated header for water coolers
 
Solution
1 x AAFP connector
1 x CPU Fan connector(s) (4 -pin)
1 x CPU OPT Fan connector(s) (4 -pin)
6 x Chassis Fan connector(s) (4 -pin)
2 x Assistant Fan connector(s) (1 x 3 -pin, 1 x 4 -pin, [White])
1 x S/PDIF out header(s)
1 x System panel(s) (Q-Connector)
1 x 5-pin EXT_FAN(Extension Fan) connector
1 x Chassis Intrusion connector(s)
3 x Thermal sensor connector(s)
1 x CPU OV
1 x Clear CMOS jumper(s)
1 x Water Pump header (4-pin)
Pages 1-7, 1-8 of the manual shows the location and function of each of those connectors. The remainder of Chapter 1 describes each connector/jumper in detail.