H-Locus
Most rat markings are created by mutations at the H-locus. The most distinctive is probably the hooded, but the full variety is quite amazing. Opinions on which alleles actually exist in the fancy at the moment differ, but some known alleles include:
| H/H | Self |
| H/h or H/He or H/Hn | Berkshire (with varying amounts of white, pictured is a standard H/h) |
| H/Hro | Essex |
| He/He or He/Hn or He/Hro | Black eyed white |
| He/He or He/Hn or He/Hro | Patched/mismarked/masked |
| He/He or He/Hn or Hn/Hn | Capped/Bareback |
| He/hi or Hn/hi | Variegated or "variberk" |
| hi/hi or H/hi | Irish |
Downunder Modifier
The downunder gene modifies the pattern of white spotting to leave a saddle (like hooded) but across the stomach. Further modifiers or combinations of H locus alleles can interact with this modifier to give a whole variety of new patterns.
| H/hdu | Downunder Berkshire |
| h/hdu | Downunder hooded |