The H-locus
The original pet/fancy rat lines' markings are caused by mutations on what we call the "hooded" locus. The best known of all these mutations is "hooded" and it was the first mutant allele known. Hoodeds are considered the "safest" of all markings, as the mutation is not associated with any health problems, and the hooded phenotype is easy to distinguish from other markings (including similar ones like banded). These gene definitions come from a few resources including the now non-existant Rodentfancy.com (I am not listing any genotypes here because none of the references I found echoed what I've seen in breeding.)
H: Self gene; Involved in self, Berkshires, Irish, and possibly variegated
h: Hooded gene; Homozygous is hooded, also in Berkshires, Irish, and possibly in barebacks and capped
He: Extreme hood gene; In Berkshires, also capped, patched, BEW, and capped
Hre: Restricted hood gene; Homozygous lethal, fades colors and causes odd-eyes, sometimes sterility in males
Hro: Roberts gene; Homozygous lethal, fades colors and causes odd-eyes
hn: Notched gene; Similar to He but always a notch at the back of a capped marking
hi: Irish gene; Mock selfs, Irish, and "Berkshire," also in variegated, and sometimes hooded
hdu: Downunder gene; Homozygous lethal, causes colored parts to be on the underside (sometimes called "double hooded")