Phenotype SNPs from Mesolithic and Neolithic Latvia and Ukraine

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for genomes from Mesolithic and Neolithic Latvia and Ukraine. Nonzero derived allele counts are in bold. Note that small derived allele counts may be due to DNA damage.

ASIP, rs2424984, Veddoid brown skin

Sample       Period            Culture      Date BC    D/T
Latvia_HG2   Mesolithic        Narva        5841–5636  7/7
Latvia_MN1   Middle Neolithic  Unassigned   4251–3976  1/1
Latvia_LN1   Late Neolithic    Corded Ware  3089–2676  0/1
Ukraine_HG1  Mesolithic        Unassigned   9193–8641  0/1

ASIP, rs6058017, Veddoid brown skin

Sample      Period            Culture      Date BC    D/T
Latvia_HG1  Mesolithic        Kunda        6467–6249  2/2
Latvia_HG2  Mesolithic        Narva        5841–5636  1/1
Latvia_HG3  Early Neolithic   Unassigned   5302–4852  2/2
Latvia_MN2  Middle Neolithic  Comb Ware    4229–3800  0/0
Latvia_LN1  Late Neolithic    Corded Ware  3089–2676  0/1

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample      Period            Culture      Date BC    D/T
Latvia_HG2  Mesolithic        Narva        5841–5636  0/4
Latvia_MN2  Middle Neolithic  Comb Ware    4229–3800  0/1
Latvia_LN1  Late Neolithic    Corded Ware  3089–2676  0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample       Period            Culture     Date BC    D/T
Latvia_HG1   Mesolithic        Kunda       6467–6249  3/3
Latvia_HG2   Mesolithic        Narva       5841–5636  4/4
Latvia_HG3   Early Neolithic   Unassigned  5302–4852  1/1
Latvia_MN2   Middle Neolithic  Comb Ware   4229–3800  0/3
Ukraine_HG1  Mesolithic        Unassigned  9193–8641  1/2

KITLG, rs12821256, blond hair

Sample      Period           Culture     Date BC    D/T
Latvia_HG1  Mesolithic       Kunda       6467–6249  0/4
Latvia_HG3  Early Neolithic  Unassigned  5302–4852  0/1

KITLG, rs642742, Veddoid brown skin

Sample      Period            Culture     Date BC    D/T
Latvia_HG2  Mesolithic        Narva       5841–5636  3/3
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  1/2
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  3/3

MC1R, rs1110400, red hair

Sample      Period            Culture    Date BC    D/T
Latvia_HG1  Mesolithic        Kunda      6467–6249  0/2
Latvia_HG2  Mesolithic        Narva      5841–5636  0/3
Latvia_MN2  Middle Neolithic  Comb Ware  4229–3800  0/1

MC1R, rs11547464, red hair

Sample       Period            Culture     Date BC    D/T
Latvia_HG1   Mesolithic        Kunda       6467–6249  0/4
Latvia_HG2   Mesolithic        Narva       5841–5636  0/4
Latvia_MN2   Middle Neolithic  Comb Ware   4229–3800  0/3
Ukraine_HG1  Mesolithic        Unassigned  9193–8641  0/1

MC1R, rs1805005, blond hair, fair skin

Sample      Period           Culture      Date BC    D/T
Latvia_HG1  Mesolithic       Kunda        6467–6249  0/3
Latvia_HG2  Mesolithic       Narva        5841–5636  0/5
Latvia_HG3  Early Neolithic  Unassigned   5302–4852  0/2
Latvia_LN1  Late Neolithic   Corded Ware  3089–2676  0/1

MC1R, rs1805006, red hair, fair skin

Sample       Period            Culture         Date BC    D/T
Latvia_HG1   Mesolithic        Kunda           6467–6249  0/1
Latvia_HG2   Mesolithic        Narva           5841–5636  0/5
Latvia_HG3   Early Neolithic   Unassigned      5302–4852  0/1
Latvia_MN2   Middle Neolithic  Comb Ware       4229–3800  0/1
Latvia_LN1   Late Neolithic    Corded Ware     3089–2676  0/1
Ukraine_HG1  Mesolithic        Unassigned      9193–8641  0/1
Ukraine_N1   Neolithic         Dnieper-Donets  4519–4343  0/1

MC1R, rs1805007, red hair, fair skin

Sample      Period            Culture    Date BC    D/T
Latvia_HG1  Mesolithic        Kunda      6467–6249  0/3
Latvia_HG2  Mesolithic        Narva      5841–5636  0/4
Latvia_MN2  Middle Neolithic  Comb Ware  4229–3800  0/3

MC1R, rs1805008, red hair, fair skin

Sample      Period      Culture  Date BC    D/T
Latvia_HG2  Mesolithic  Narva    5841–5636  0/6

MC1R, rs1805009, red hair, fair skin

Sample      Period           Culture     Date BC    D/T
Latvia_HG1  Mesolithic       Kunda       6467–6249  0/2
Latvia_HG2  Mesolithic       Narva       5841–5636  0/4
Latvia_HG3  Early Neolithic  Unassigned  5302–4852  0/2

MCM6, rs182549, ability to digest milk

Sample      Period            Culture     Date BC    D/T
Latvia_HG1  Mesolithic        Kunda       6467–6249  0/2
Latvia_HG2  Mesolithic        Narva       5841–5636  0/3
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  0/1
Latvia_MN1  Middle Neolithic  Unassigned  4251–3976  0/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  0/3

MCM6, rs4988235, ability to digest milk

Sample      Period            Culture     Date BC    D/T
Latvia_HG2  Mesolithic        Narva       5841–5636  0/1
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  0/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  0/3

OCA2, rs1800407, green or hazel eyes

Sample      Period            Culture    Date BC    D/T
Latvia_HG2  Mesolithic        Narva      5841–5636  1/4
Latvia_MN2  Middle Neolithic  Comb Ware  4229–3800  0/2

OCA2, rs1800414, Mongoloid light skin

Sample      Period            Culture     Date BC    D/T
Latvia_HG1  Mesolithic        Kunda       6467–6249  0/1
Latvia_HG2  Mesolithic        Narva       5841–5636  0/4
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  0/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  0/1

OCA2/HERC2, rs12913832, blue eyes

Sample      Period            Culture     Date BC    D/T
Latvia_HG1  Mesolithic        Kunda       6467–6249  0/1
Latvia_HG2  Mesolithic        Narva       5841–5636  4/4
Latvia_MN1  Middle Neolithic  Unassigned  4251–3976  1/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  0/1

SLC24A5, rs1426654, Caucasoid light skin

Sample      Period            Culture     Date BC    D/T
Latvia_HG1  Mesolithic        Kunda       6467–6249  0/1
Latvia_HG2  Mesolithic        Narva       5841–5636  0/5
Latvia_HG3  Early Neolithic   Unassigned  5302–4852  1/1
Latvia_MN2  Middle Neolithic  Comb Ware   4229–3800  1/1

SLC45A2, rs16891982, Caucasoid light skin

Sample      Period            Culture         Date BC    D/T
Latvia_HG1  Mesolithic        Kunda           6467–6249  0/1
Latvia_HG2  Mesolithic        Narva           5841–5636  0/3
Latvia_HG3  Early Neolithic   Unassigned      5302–4852  0/1
Latvia_MN2  Middle Neolithic  Comb Ware       4229–3800  1/1
Ukraine_N1  Neolithic         Dnieper-Donets  4519–4343  1/1

TYR, rs1042602, light skin, absence of freckles

Sample       Period            Culture      Date BC    D/T
Latvia_HG1   Mesolithic        Kunda        6467–6249  0/2
Latvia_HG2   Mesolithic        Narva        5841–5636  0/2
Latvia_HG3   Early Neolithic   Unassigned   5302–4852  0/1
Latvia_MN2   Middle Neolithic  Comb Ware    4229–3800  0/2
Latvia_LN1   Late Neolithic    Corded Ware  3089–2676  0/1
Ukraine_HG1  Mesolithic        Unassigned   9193–8641  0/2

TYR, rs1393350, blond hair, blue eyes

Sample       Period            Culture         Date BC    D/T
Latvia_HG2   Mesolithic        Narva           5841–5636  0/1
Latvia_HG3   Early Neolithic   Unassigned      5302–4852  0/2
Latvia_MN2   Middle Neolithic  Comb Ware       4229–3800  0/1
Latvia_LN1   Late Neolithic    Corded Ware     3089–2676  0/1
Ukraine_HG1  Mesolithic        Unassigned      9193–8641  0/2
Ukraine_N1   Neolithic         Dnieper-Donets  4519–4343  0/2

TYRP1, rs2733831, light hair and eyes

Sample      Period            Culture    Date BC    D/T
Latvia_HG1  Mesolithic        Kunda      6467–6249  1/3
Latvia_HG2  Mesolithic        Narva      5841–5636  2/5
Latvia_MN2  Middle Neolithic  Comb Ware  4229–3800  2/2
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4 comments on “Phenotype SNPs from Mesolithic and Neolithic Latvia and Ukraine
  1. Anon says:

    Why no calls for the two Ukrainian HG light skin SNPs? The paper claimed they were derived for both SLC24 and SLC45, also claimed Latvian HG1 had blue eyes and Latvia MN1 was blonde.

    • Genetiker says:

      The genotypes in the paper were probabilistically imputed using data for nearby SNPs. The results in this post are based only on data for the phenotype SNPs themselves.

  2. Capra Internetensis says:

    The chart in the paper marks the mutations which were actually read with a star, or two stars for multiple reads.

    But it is good to have explicit numbers. Thank you.

  3. How these SNP relevant and keeping up to date on https://snpedia.com/ ?
    Eg. I see this https://www.snpedia.com/index.php/Rs182549 and realize part of described information there.
    I mean, if u write some SNPs here, does it mean it’s kinda new invented or simply recognized in new DNA material?

    PS. I’m not sure yet how this all work in Mesolithic DNA research.

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