Random encounters, Treasure Chest, Pillar of Abundance
They are of six levels represented by different color. Each one being craftable by combining 3 runes of the previous level. The level of a rune is also recognizable by its color:
(Most powerful Runes)
There are different kinds of recipes available, all of which has different runes requirement (Numbers and Color). It is also worth noting that once combined, they cannot be broken back to 3 runes of a lower level.
As a consequence, combining all them to stronger runes is often a bad idea, as you may need runes of lower level at some point to cast specific spells.