I currently have been playing Cho'gath a lot and really like the AP build for him.

What is the best RUNE BUILD for an AP CHO'GATH?

Red attack speed, quint move or AS, yellow and blue clarity.

dun listen to the kid who tells u that **** for ap cho'gath
get these

AP if u fill all rune slots ull get bonus 85 at lvl 18

magic pen good for early does more dmg u wont need much most ppl go glass dps therefore almost no magic def

Less cooldown- dun use this ever never found that .5 sec to be useful .5-3 depending on ulties etc

i would suggest ap mostly since it raises your ults hp also

All flat HP runes, in every slot. Start out with 800+ life at lvl 1. See how they deal with you then .