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On my rune pages each seems to have a halo under it, but occasionally with a different color from that of the mark/seal/glyph it's in. What does it mean?

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Here's a list of primary runes: – Ryre Oct 27 '11 at 16:08
up vote 14 down vote accepted

Each stat has a particular type of rune that it is best with. Even if it is available on other runes, it will only have a weaker effect in comparison. You can see the full list of these compatibilities in this answer. Generally, it is optimal to go for these "primary" runes, but a certain strategies do revolve around using "secondary" rune types.

The "halo" effect shows you what the primary rune type for that particular stat is. So for example, if you have a Greater Glyph of Strength, it will have a Red halo, because the best rune type for Attack Damage is the Mark (Red). Seals of Strength would also have a Red halo.

Quintessences will always glow the color of one of the other three runes unless it is one of the stats that is only available on a Quintessence. So a Quintessence of Fortitude will glow Yellow as Health is generally a Seal. But a Quintessence of Swiftness will glow purple, as movespeed is only available on Quintessences.

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