Currently, there are 6 different runes in the game. Each rune can either improve your TAP damages or your DPS. At the begining of each game, only the first two runes are available for use: Kha and Eyr. You can unlock the others by buying them with gold throughout your progress. There is only one rune for TAP and five runes for DPS.
"Over the centuries, The Order has studied and deciphered thousands of Runes used by the Arai. Most of these studies have been inconsequential, but every now and then the relentless scrutiny yields a notable find. These powerful Runes can be instilled into objects or weapons, granting their wielders access to unspeakable powers.
The Runes come in two categories. The TAP Rune inflicts damage with each stroke of the blade. The DPS (damage-per-second) Rune automatically delivers continuous damage against the enemy during the attack."
Upon reaching level 5 in any rune, you unlock a new Spell. For players who prefer using TAP, you should focus only on Kha. DPS-specializing players will have to find out which rune is the most effective for its cost.
Each time you reach 100 levels for a rune, its symbol will glow a bit more.