You can obtain runes by killing Bosses, completing quests or from other tasks. To use the rune, drag it and place it on the desired item.
Note: Runes are divided in 3 tiers of rarity,  Common, Uncommon and Rare.

Padded : [Boots Only] Decreases fall damage by 1.00 to 3.00.

Insulating : Decreases fire/debuff damage by 30.0% to 80.0%.

Prickly : [Chestplate Only] Every 1 to 3 hits, deals back 5.00 to 10.00% damage to enemy.

Deflecting : Decreases ranged damage by 0.50 to 1.50.

Blunting : Decreases melee damage by 0.50 to 1.50.

Of the Berserker : Increases melee damage dealt by 0.50 to 1.00. Increases incoming damage by 0.50 to 1.50.

Of the Paladin : Decreases melee damage dealt by 0.50 to 1.00. Decreases incoming damage by 0.50 to 1.50.

Of the Hunter : Decreases damage from mobs by 1.00 to 2.00.

Of Mending : Passively regenerates durability over time. Note : 1 durability per 5 seconds when held or worn.