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F is the flaxen locus. The recessive allele when homozygous (ff) produces flaxen manes and tails on red based horses. Ff or FF produces non-flaxen red based horses. Neither allele has any effect on black based horses.

S is the sooty locus. It has 3 alleles in the game. S is non-sooty. Ssty is normal sooty which darkens the horse from the top down on both red and black based horses. S+ causes dark dapples and intensifies the effect of dun. Homozygous sooty (Ssty or S+) is darker than heterozygous.
S+ buckskin
S+ red dun

Kit is a gene with multiple alleles causing various spotting patterns. It is also responsible for a variety of vital functions. Several of the kit alleles are lethal when homozygous or combined because a horse requires at least one copy that is largely intact or it dies early in embryonic development.
The kit mutations are:
Kitr -- roan. Safe when homozygous and with all other Kit mutations.
Kitto -- tobiano. Safe when homozygous and with all other Kit mutations.
Kitsb -- sabino. There are 3 sabinos in the game. All are safe and produce more extensive white markings when homozygous or combined with each other. Sb1 and Sb2 are lethal when combined with white 1 and 2.
Heterozygous Sb1
Homozygous Sb1
Heterozygous Sb2
Heterozygous Sb3
Kitw -- dominant white. There are 4 whites in the game. All are lethal when homozygous or combined with each other. White 1 and 2 are lethal with Sb1 and 2.
White 1
White 2
White 3
White 4

PAX3 is the splash 2 locus. PAX3+ is non-splash. PAX3C70Y is splash 2.
Sp is splash 1 and 3. Sp is non-splash. Sps is splash 1 and Sp3 is splash 3.
Here is the link to Ammit's announcement of the recent addition of splash 2 and 3: http://www.huntandjump.com/forum.php#/discussion/3042/3-million-horse-surprise-not-one-gene-but-two-and-new-art-for-all-splash-horses-

Vrn is varnish. When combined with appaloosa it causes the progressive varnishing of the horse as it ages. Vrn is dominant to non-varnish (V). Varnish has no effect on non-appaloosas.

L is leopard complex (appaloosa). L is non-appaloosa. Llp is appaloosa. Heterozygous LlpL produces a white blanket with spots. Homozygous LlpLlp produces a blanket with no spots. Appaloosas also often have mottled skin on the muzzle and striped hooves.

PATN controls the size of the appaloosa blanket on horses with Llp. It ranges from PATN: Extensive which produces leopard apps to PATN: None which produces horses with no blanket, only the mottled muzzle and striped hooves.

O is the frame locus. O is non-frame. Olw is frame (overo lethal white). It is lethal when homozygous (in real life the foals are born alive, solid white, with incomplete digestive tracts and die of impaction colic shortly after birth). Frame changes the expression of splash, sabino and white, but has no visible effect on it's own, so it is important to color test for it if you are breeding to a horse that has it.

I is the fantasy gene ice. IiIi is non-ice. There are several ice alleles with ice 1 (II) being the most common.
http://www.huntandjump.com/horse.php?horseid=3027306

Rb is rabicano. rbrb is non-rabicano. Rabicano is dominant. It causes roaning in the flank and at the top of the tail.
http://www.huntandjump.com/horse.php?horseid=2115488

WF is white factor. It controls the expression of all the non-appaloosa pattern genes and the normal white leg and face markings in the same way PATN controls the size of appaloosa markings.