This is about as close to the full genetics as things get right now for breeders online. Dr. Sponenberg has a book, Equine Color Genetics, which goes into greater detail. His theories appear more extensive but less clearly explained than Dr. Bowling's. This is a combination of the two gene theories presented in Dr. Bowling's clearer format.

To begin with, you need a basic understanding of heredity. If you need a quick lesson in genetics and heredity, Wikipedia's article on alleles or this tutorial on inheritance can help you.

Note: for references to melanin (pigment or coloring): There are two chemically distinct types of melanin: the red–yellow phaeomelanin and the brown–black eumelanin. All coloration genes in mammals affect either the production or final effect of these two chemicals.
Note 2: The terms Alleles and Modifiers are used interchangeably in this report.
Note 3: Socks, Star, Strip, and Snip genetics are not yet fully understood but probably multiple allele influenced.

Alleles
Effect of Combined Pairs of Alleles

W
W

w

The existence of a specific W gene is questioned by some. Lethal White as a genetic syndrome is accepted universally.

WW: Lethal (Results in incomplete colon and the inability to defecate. Probably from a gene near W or O but not influencing the color directly.)

Ww: Horse typically lacks pigment in skin, hair and eyes and appears to be white.

ww: Horse is fully pigmented.

G

G

g
GG or Gg: Horse shows progressive slivering with age to white or flea-bitten, but is born a non-gray color. Pigment is always present in skin and eyes at all stages of silvering. Gray colors range from white to dark gray as they do in human hair.

gg: Horse does not gray with aging.

E E
e
EE or Ee: Horse forms black pigment in skin and hair. Black pigment in hair may be either in a points pattern or uniformly distributed.

ee: Horse has black pigment in skin, but red pigment in hair. Horse will not appear red if white, gray, roaning, or dilution genes are present.

E+ E+

e+
E+E+ or E+e+ Dominant black, non-fading –Overrides the A or bay allele resulting in all black horse
e+e+ no effect

A A
a

Agouti-Bay: Acts on "E" to restrict eumelanin, or black pigment, to points. Has no effect on "e" or red.

AA or Aa: If horse has black hair (E not E+), then that black hair shows only in points pattern.

aa: If horse has E allele, then horse will be uniformly black..

C

C

Ccr Also noted as 'c'

CCcr Palomino CC: Horse is fully pigmented.

CCcr: Red pigment is diluted to yellow; black pigment is unaffected

CcrCcr:

CcrCcr

CcrCcr: Both red and black pigments are diluted to pale cream. Skin and eye color are also diluted.

D D
d

DD or Dd: Dun Horse shows a diluted body color to pinkish-red, yellow-red, yellow or mouse gray and has dark points including dorsal stripe, shoulder stripe and leg barring.

dd: Horse has undiluted coat color.

TO TO
to

TOTO or Toto: Produces regular and distinct ovals or round patterns of white and color that extend down over the neck and chest, giving the appearance of a shield.

toto: No tobiano pattern present.

O Also noted as Fr or FrO O
o

OO or Oo: Overo or Frame Overo pattern --color forms a frame around white patterning. Overo as an allele is different from overo as a registration since the registration also includes the splash and sabino alleles. Homozygous associated with lethal white syndrome.

oo: No overo pattern present

Ch Ch
ch

Champagne: A rare dilution gene that creates pumpkin-colored freckled skin, amber or blue eyes, and gives a bronze cast to hair. The skin surrounding the eye must be pink with freckles. A champagne horse is born with a darker foal coat that lightens with maturity.
ChCh or Chch: champagne dilution evident (See Genetic Formulas Chart below.)

chch: no champagne dilution

F F
f
Effects visible on red or chestnut colors only.

FF or Ff: Red points on ee horses

ff: flaxen points on ee horses

P P
p

Pangare (Mealy) The effects of this allele appear along the underside of the horse, in the "soft" parts, or on the muzzle, behind the elbows, in the flanks, on the buttock, above or around the eyes, and along the belly.

PP or Pp: Mealy or Pangare dilution of pigment

pp: no mealy looking lightening of pigment

Rn Rn
rn

RnRn or Rnrn: roan pattern of white hair mixed in with base color. There is no lethal roan. (*See footnote.)

rnrn: no roan pattern

Rb Rb
rb

Rabicano: Partial roaning with 'coon' tail markings. Thought to be a dominate gene by Sponenberg.

RbRb or Rbrb: rabicano markings

rbrb: no rabicano traits

Sb Sb
sb

Sabino Feathery Misty of Chincoteague like white markings.

Only paint marking pattern found in full blooded Arabians. Sabino may well be polygenic and causes abundant white on the legs, and then creeps up as belly spots and body spots that are can be flecked and roaned. Sabino is registered as overo but does not entail the overo or frame overo allele. No risk of lethal white.

SbSb or Sbsb: sabino markings

sbsb: no sabino marks

Spl Spl
spl

Splash, Splashed White

Looks like reverse tobiano with white moving from the bottom of the horse towards the top. The horses head will look as if dunked in bucket of white paint. White coloring appears to move boldly and smoothly from bottom up.

SplSpl or Splspl: Splashed markings. Spash is registered as overo but has does not entail the overo or frame overo allele and is not associated with lethal white syndrome.

splspl: no splashed markings

Sty Sty
sty

Sooty

StySty or Stysty: black mixed into body coat.

stysty: no black mixed into coat

Z also noted as S Z
z

ZZ or Zz: Silver dapple - dilutes eumelanin or black pigment. Converts black to brown with white mane and tail or results in silver coloring.

zz: no silver dapple

LpOp

Appaloosa spotting gene. This gene is inferred and the inference is disputed. Sponenberg is in favor of its existence. Others maintain that it is a multiple allele trait.

Chart based on Dr. Bowling's Genetic Formulas
Partial list of Genetic Formulas and Color Definitions
Genetic Formula
Color

W
White

G
Gray (Insert Anisa picture)

E, A, CC, dd, gg, ww, toto
Bay or Brown

E, aa, CC, dd, gg, ww, toto
Black (Insert Sarah pic.)

ee, aa, CC, dd, gg, ww, toto
Red: Sorrel or Chestnut (Insert Ofi picture)

E, A, CCcr, dd, gg, ww, toto
Buckskin

ee, CCcr, dd, gg, ww, toto
Palomino

ee, CcrCcr
Cremello

E, CcrCcr
Perlino

E, A, CC, D, gg, ww, toto
Buckskin Dun

E, aa, CC, D, gg, ww, toto
Mouse Dun or Grulla

E,A,CC,D
Dun, Zebra Dun, Bay Dun, Classic Dun

ee, CC, D, gg, ww, toto
Red Dun

gg, E, aa, CC, dd, RN
Black Roan (Blue Roan)

gg, E, A, CC, dd, RN
Bay Roan (Insert Lancer picture)

gg, ee, CC, dd, RN
Red Roan (Insert Merryberry pic)

gg, E, A, CCcr, dd, RN
Buckskin Roan (Red Roan)

gg, ee, CCcr, dd, RN
Palomino Roan (Red Roan)

gg, E, A, CC, D, RN
Buckskin Roan (Red Roan)

gg, E, aa, CC, D, RN
Mouse Dun Roan, Grulla Roan, or Blue Roan

gg,ee, CC, D, RN
Red Dun Roan (Red Roan)

gg, E, A, CC, dd, gg, ww, TO
Bay Tobiano

gg, ee, CC, D, gg, ww, TO
Red Dun Tobiano

gg, Ch, ee, aa, CC, dd, gg, ww, toto
Gold--looks like Palomino

gg, Ch, E, A, CC, dd, gg, ww, toto
Amber

gg, Ch, E, aa, CC, dd, gg, ww, toto
Champagne

gg, Ch, ee, CcrCcr
Ivory

gg, E, aa, CC, dd, TO, Sb
Black Sabino-Tobiano (Tovero without lethal white.) (Insert Magic pic.)

gg, E, aa, CC, dd, TO, O
Black Tobiano-Overo (Tovero carrying lethal white.)

ee, CCcr, dd, gg, ww, TO
Palomino Tobiano Paint (Insert Rain pic.)

gg, ee, aa, CC, dd, TO, Spl
Red Tobiano-Splash (Tovero without lethal white.)

*Lethal Roan Question:

Hintz, H.F. and VanVleck, L.D., published 1979. Lethal Dominant Roan in Horses. Journal of Heredity 70:145-146. This study, based on percentages of roan foals thrown by roan parents, popularized the idea of Lethal Roan Syndrome. The study did not include direct genetic analysis and assumed fetus absorption preventing birth.

A recent genetic study of roans by Dr. Bowling (See http://www.hancockhorses.com/article-roanQHNews.pdf) refuted Hintz and VanVleck's inferences. Using genetic analysis, Dr. Bowling found several homozygous roans and no evidence of a Lethal Roan Syndrome.