Hi there! This is my first guide posted here and I hope it will help people play this rider in the best way possible.

Runes are important on Sejuani cause they have a big impact on her early and late game.
- All of Sejuani's abilities do magic damage and thats why I use magic penetration as marks, bursts your damage early on and helps you a bit for the whole game.
Greater Seal of Vitality - Sejuani's W does scale with ability power and your maximum health. Also compliments your role as tank with more health.
- We are playing a tanky character who should be in the middle of the battle and thats why I take magic resistance to help me survive more spells casted on me.
Greater Quintessence of Vitality - Again, tankiness and a big burst to your W damage.

Percentage vs. Flat Numbers

Before I tell you the logic behind the choice I'll show you the math:
Greater Quintessence of Vitality and Greater Seal of Vitality will both grant you 320.76 health at level 18 regardless of your gear.
Greater Seal of Endurance and Greater Quintessence of Endurance together those runes grant you 9% boost to your maximum health. Which is if you have 4000 health will be 360.
What means that the percentage runes will be better after you have more then 3564 health. Otherwise you will get smaller bonus then from the Vitality runes may give you.

Now the logic is that you can switch to percentage runes when you know that you will be able to come to the mid-late game can have your equipment on you. Then your runes will payout.
This is possible to predict when playing in draft pick mode and by analyzing your and the enemy team.