At high levels some classes give a character subtle powers like foresight, limited telepathy or words of command.
As Dwarves advance in level they can choose three spells related to runes for opening/closing doors or relaying secrets. These spells are chosen at the expense of other features.
Elves have three spells available as well as they advance in level, but they are far less powerful than typical D&D spells.
Some rare items are described that give bonuses due to their special background, dwarven armour and weapons for example.
The most supernatural aspect is a game device called The Shadow. I hear that it works like Insanity rules in Cthulu games where it can gradually corrupt characters who experience or perpetrate wicked deeds.