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
Genetiker 
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.
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.
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.
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.