Pigmentation SNP genotypes for prehistoric Swedes

Below are all of the available genotypes from the prehistoric Swedes for the pigmentation SNPs included in the 8-plex and HIrisPlex systems.

Ajvide 58 and Gökhem 2 both had two copies of the derived allele for rs12913832, so they both very likely had blue eyes.

None of the samples had derived alleles for rs1805007, rs1805008, or rs1805009, which are associated with red hair.

None of the samples had the derived allele for rs12821256, which is associated with blond hair.

Neither Ajvide 58 nor Gökhem 2 had the derived allele for rs1042602, which is associated with light skin.

Gene        SNP         Sample           Genotype
ASIP        rs6119471   Ajvide 58        CC
ASIP        rs6119471   Ajvide 70        CC
ASIP        rs6119471   Gökhem 2         CC
EXOC2       rs4959270   Ajvide 52        CC
EXOC2       rs4959270   Ajvide 58        CA
EXOC2       rs4959270   Ajvide 70        AA
EXOC2       rs4959270   Gökhem 2         CC
IRF4        rs12203592  Ajvide 58        TC
IRF4        rs12203592  Gökhem 2         CC
KITLG       rs12821256  Ajvide 58        TT
KITLG       rs12821256  Gökhem 2         TT
KITLG       rs12821256  Gökhem 4         TT
MC1R        rs1110400   Ajvide 58        TT
MC1R        rs1110400   Gökhem 2         TT
MC1R        rs1110400   Gökhem 7         TT
MC1R        rs1110400   Stora Förvar 11  TT
MC1R        rs11547464  Ajvide 58        GG
MC1R        rs11547464  Gökhem 2         GG
MC1R        rs11547464  Stora Förvar 11  GG
MC1R        rs1805005   Ajvide 58        GG
MC1R        rs1805005   Gökhem 2         GG
MC1R        rs1805006   Ajvide 58        CC
MC1R        rs1805006   Gökhem 2         CC
MC1R        rs1805007   Ajvide 58        CC
MC1R        rs1805007   Gökhem 2         CC
MC1R        rs1805007   Gökhem 7         CC
MC1R        rs1805007   Stora Förvar 11  CC
MC1R        rs1805008   Ajvide 58        CC
MC1R        rs1805008   Gökhem 2         CC
MC1R        rs1805008   Gökhem 7         CC
MC1R        rs1805008   Stora Förvar 11  CC
MC1R        rs1805009   Ajvide 58        GG
MC1R        rs1805009   Gökhem 2         GG
MC1R        rs2228479   Ajvide 58        GG
MC1R        rs885479    Ajvide 58        GG
MC1R        rs885479    Gökhem 2         GG
MC1R        rs885479    Gökhem 7         GG
MC1R        rs885479    Stora Förvar 11  GG
OCA2/HERC2  rs12913832  Ajvide 58        GG
OCA2/HERC2  rs12913832  Gökhem 2         GG
OCA2        rs1545397   Ajvide 58        AA
OCA2        rs1545397   Ajvide 70        AA
OCA2        rs1545397   Ire 8            AA
OCA2        rs1800407   Ajvide 58        CC
OCA2        rs1800407   Gökhem 2         CC
PIGU/ASIP   rs2378249   Ajvide 58        AA
PIGU/ASIP   rs2378249   Gökhem 2         AA
SLC24A4     rs12896399  Ajvide 58        TT
SLC24A4     rs12896399  Gökhem 2         TT
SLC24A4     rs2402130   Ajvide 58        AA
SLC24A4     rs2402130   Ajvide 70        AA
SLC24A4     rs2402130   Gökhem 2         AA
SLC24A5     rs1426654   Ajvide 58        GG
SLC24A5     rs1426654   Gökhem 2         AA
SLC45A2     rs16891982  Ajvide 58        CC
SLC45A2     rs16891982  Gökhem 2         GG
SLC45A2     rs16891982  Stora Förvar 11  GG
SLC45A2     rs28777     Ajvide 52        CC
SLC45A2     rs28777     Ajvide 58        CT
SLC45A2     rs28777     Gökhem 2         AA
TYR         rs1042602   Ajvide 58        CC
TYR         rs1042602   Gökhem 2         CC
TYR         rs1393350   Ajvide 52        GG
TYR         rs1393350   Ajvide 58        GG
TYR         rs1393350   Gökhem 2         GG
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3 comments on “Pigmentation SNP genotypes for prehistoric Swedes
  1. banti says:

    Great job.
    But rs1042602 has nothing to do with skin pigmentation (light) it is just associated with freckling. Skin pigmentation (light) is determined by rs16891982 G/G and rs1426654 A/A.

    Gok2 has an interesting eye color being rs12913832 G/G (not Brown) but rs12203592 C/C (not T/T) and therefor not Blue.

    It is the same picture as with all other prehistoric samples:
    the Hunter-Gatherer is dark skin, dark hair and light eyes
    the Farmer is light skin, dark hair and (a novelty) not dark eyes

    • genetiker says:

      But rs1042602 has nothing to do with skin pigmentation (light) it is just associated with freckling.

      No.

      From the Wikipedia article on human skin color:

      “The TYR gene encodes the enzyme tyrosinase, which is involved in the production of melanin from tyrosine. It has an allele, Ser192Tyr (rs1042602[46]), found solely in 40–50% of Europeans[15][16] and linked to light-colored skin in studies of both mixed-race South Asian[41] and African-American[47] populations.”

      41 is a reference to this paper and 47 is a reference to this paper.

  2. banti says:

    Based on the ”two-step procedure” of the 8plex system however Gok2 is considered to have Blue eyes due to her rs12896399 T/T in combo with her rs12913832 G/G. Meaning the first light (Blue) eye Farmer.

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