Phenotype SNPs from prehistoric Portugal

Below are genotypes for SNPs that have a large effect on phenotype for 10 genomes from prehistoric Portugal. Genotypes with derived alleles are highlighted.

ASIP, rs2424984, Veddoid brown skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 TT
LC42 Middle Neolithic 4200–3500 CT
LC44 Middle Neolithic 4200–3500 TT
CA122A Copper Age 3500–2000 TT
CM364 Copper Age 3500–2000 TT
CM9B Copper Age 3500–2000 TT
DA96B Copper Age 3500–2000 TT
MG104 Middle Bronze Age 1740–1430 TT
TV32032 Middle Bronze Age 1740–1430 TT
TV3831 Middle Bronze Age 1740–1430 TT

ASIP, rs6058017, Veddoid brown skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 AA
LC42 Middle Neolithic 4200–3500 GA
LC44 Middle Neolithic 4200–3500 AA
CA122A Copper Age 3500–2000 AA
CM364 Copper Age 3500–2000 AA
CM9B Copper Age 3500–2000 AA
DA96B Copper Age 3500–2000 AA
MG104 Middle Bronze Age 1740–1430 AA
TV32032 Middle Bronze Age 1740–1430 AA
TV3831 Middle Bronze Age 1740–1430 AA

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 AA
LC42 Middle Neolithic 4200–3500 AA
LC44 Middle Neolithic 4200–3500 AA
CA122A Copper Age 3500–2000 AA
CM364 Copper Age 3500–2000 AA
CM9B Copper Age 3500–2000 AA
DA96B Copper Age 3500–2000 AA
MG104 Middle Bronze Age 1740–1430 AA
TV32032 Middle Bronze Age 1740–1430 AA
TV3831 Middle Bronze Age 1740–1430 AA

IRF4, rs12203592, light hair and eyes, freckling

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 CC
LC42 Middle Neolithic 4200–3500 CC
LC44 Middle Neolithic 4200–3500 CC
CA122A Copper Age 3500–2000 CC
CM364 Copper Age 3500–2000 CC
CM9B Copper Age 3500–2000 CC
DA96B Copper Age 3500–2000 CC
MG104 Middle Bronze Age 1740–1430 CC
TV32032 Middle Bronze Age 1740–1430 CC
TV3831 Middle Bronze Age 1740–1430 CC

KITLG, rs12821256, blond hair

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 TT
LC42 Middle Neolithic 4200–3500 TT
LC44 Middle Neolithic 4200–3500 TT
CA122A Copper Age 3500–2000 TT
CM364 Copper Age 3500–2000 TT
CM9B Copper Age 3500–2000 TT
DA96B Copper Age 3500–2000 TT
MG104 Middle Bronze Age 1740–1430 TT
TV32032 Middle Bronze Age 1740–1430 TT
TV3831 Middle Bronze Age 1740–1430 TT

KITLG, rs642742, Veddoid brown skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 TC
LC42 Middle Neolithic 4200–3500 TC
LC44 Middle Neolithic 4200–3500 TC
CA122A Copper Age 3500–2000 CC
CM364 Copper Age 3500–2000 CC
CM9B Copper Age 3500–2000 TC
DA96B Copper Age 3500–2000 CC
MG104 Middle Bronze Age 1740–1430 TC
TV32032 Middle Bronze Age 1740–1430 CC
TV3831 Middle Bronze Age 1740–1430 CC

MC1R, rs1110400, red hair

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 TT
LC42 Middle Neolithic 4200–3500 TT
LC44 Middle Neolithic 4200–3500 TT
CA122A Copper Age 3500–2000 TT
CM364 Copper Age 3500–2000 TT
CM9B Copper Age 3500–2000 TT
DA96B Copper Age 3500–2000 TT
MG104 Middle Bronze Age 1740–1430 TT
TV32032 Middle Bronze Age 1740–1430 TT
TV3831 Middle Bronze Age 1740–1430 TT

MC1R, rs11547464, red hair

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 GG
LC42 Middle Neolithic 4200–3500 GG
LC44 Middle Neolithic 4200–3500 GG
CA122A Copper Age 3500–2000 GG
CM364 Copper Age 3500–2000 GG
CM9B Copper Age 3500–2000 GG
DA96B Copper Age 3500–2000 GG
MG104 Middle Bronze Age 1740–1430 GG
TV32032 Middle Bronze Age 1740–1430 GG
TV3831 Middle Bronze Age 1740–1430 GG

MC1R, rs1805005, blond hair, fair skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 GG
LC42 Middle Neolithic 4200–3500 TG
LC44 Middle Neolithic 4200–3500 GG
CA122A Copper Age 3500–2000 GG
CM364 Copper Age 3500–2000 GG
CM9B Copper Age 3500–2000 GG
DA96B Copper Age 3500–2000 GG
MG104 Middle Bronze Age 1740–1430 GG
TV32032 Middle Bronze Age 1740–1430 GG
TV3831 Middle Bronze Age 1740–1430 GG

MC1R, rs1805006, red hair, fair skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 CC
LC42 Middle Neolithic 4200–3500 CC
LC44 Middle Neolithic 4200–3500 CC
CA122A Copper Age 3500–2000 CC
CM364 Copper Age 3500–2000 CC
CM9B Copper Age 3500–2000 CC
DA96B Copper Age 3500–2000 CC
MG104 Middle Bronze Age 1740–1430 CC
TV32032 Middle Bronze Age 1740–1430 CC
TV3831 Middle Bronze Age 1740–1430 CC

MC1R, rs1805007, red hair, fair skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 CC
LC42 Middle Neolithic 4200–3500 CC
LC44 Middle Neolithic 4200–3500 CC
CA122A Copper Age 3500–2000 CC
CM364 Copper Age 3500–2000 CC
CM9B Copper Age 3500–2000 CC
DA96B Copper Age 3500–2000 CC
MG104 Middle Bronze Age 1740–1430 CC
TV32032 Middle Bronze Age 1740–1430 CC
TV3831 Middle Bronze Age 1740–1430 CC

MC1R, rs1805008, red hair, fair skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 CC
LC42 Middle Neolithic 4200–3500 CC
LC44 Middle Neolithic 4200–3500 CC
CA122A Copper Age 3500–2000 CC
CM364 Copper Age 3500–2000 CC
CM9B Copper Age 3500–2000 CC
DA96B Copper Age 3500–2000 CC
MG104 Middle Bronze Age 1740–1430 CC
TV32032 Middle Bronze Age 1740–1430 CC
TV3831 Middle Bronze Age 1740–1430 CC

MC1R, rs1805009, red hair, fair skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 GG
LC42 Middle Neolithic 4200–3500 GG
LC44 Middle Neolithic 4200–3500 GG
CA122A Copper Age 3500–2000 GG
CM364 Copper Age 3500–2000 GG
CM9B Copper Age 3500–2000 GG
DA96B Copper Age 3500–2000 GG
MG104 Middle Bronze Age 1740–1430 GG
TV32032 Middle Bronze Age 1740–1430 GG
TV3831 Middle Bronze Age 1740–1430 GG

MCM6, rs182549, ability to digest milk

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 CC
LC42 Middle Neolithic 4200–3500 CC
LC44 Middle Neolithic 4200–3500 CC
CA122A Copper Age 3500–2000 CC
CM364 Copper Age 3500–2000 CC
CM9B Copper Age 3500–2000 CC
DA96B Copper Age 3500–2000 CC
MG104 Middle Bronze Age 1740–1430 CC
TV32032 Middle Bronze Age 1740–1430 CC
TV3831 Middle Bronze Age 1740–1430 CC

MCM6, rs4988235, ability to digest milk

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 GG
LC42 Middle Neolithic 4200–3500 GG
LC44 Middle Neolithic 4200–3500 GG
CA122A Copper Age 3500–2000 GG
CM364 Copper Age 3500–2000 GG
CM9B Copper Age 3500–2000 GG
DA96B Copper Age 3500–2000 GG
MG104 Middle Bronze Age 1740–1430 GG
TV32032 Middle Bronze Age 1740–1430 GG
TV3831 Middle Bronze Age 1740–1430 GG

OCA2, rs1800407, green or hazel eyes

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 CC
LC42 Middle Neolithic 4200–3500 CC
LC44 Middle Neolithic 4200–3500 CC
CA122A Copper Age 3500–2000 CC
CM364 Copper Age 3500–2000 CC
CM9B Copper Age 3500–2000 CC
DA96B Copper Age 3500–2000 CC
MG104 Middle Bronze Age 1740–1430 CC
TV32032 Middle Bronze Age 1740–1430 CC
TV3831 Middle Bronze Age 1740–1430 CC

OCA2, rs1800414, Mongoloid light skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 TT
LC42 Middle Neolithic 4200–3500 TT
LC44 Middle Neolithic 4200–3500 TT
CA122A Copper Age 3500–2000 TT
CM364 Copper Age 3500–2000 TT
CM9B Copper Age 3500–2000 TT
DA96B Copper Age 3500–2000 TT
MG104 Middle Bronze Age 1740–1430 TT
TV32032 Middle Bronze Age 1740–1430 TT
TV3831 Middle Bronze Age 1740–1430 TT

OCA2/HERC2, rs12913832, blue eyes

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 AA
LC42 Middle Neolithic 4200–3500 AA
LC44 Middle Neolithic 4200–3500 GG
CA122A Copper Age 3500–2000 AA
CM364 Copper Age 3500–2000 AA
CM9B Copper Age 3500–2000 AA
DA96B Copper Age 3500–2000 AA
MG104 Middle Bronze Age 1740–1430 GA
TV32032 Middle Bronze Age 1740–1430 GG
TV3831 Middle Bronze Age 1740–1430 AA

SLC24A5, rs1426654, Caucasoid light skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 AA
LC42 Middle Neolithic 4200–3500 AA
LC44 Middle Neolithic 4200–3500 AA
CA122A Copper Age 3500–2000 AA
CM364 Copper Age 3500–2000 AA
CM9B Copper Age 3500–2000 AA
DA96B Copper Age 3500–2000 AA
MG104 Middle Bronze Age 1740–1430 AA
TV32032 Middle Bronze Age 1740–1430 AA
TV3831 Middle Bronze Age 1740–1430 AA

SLC45A2, rs16891982, Caucasoid light skin

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 CC
LC42 Middle Neolithic 4200–3500 GC
LC44 Middle Neolithic 4200–3500 CC
CA122A Copper Age 3500–2000 CC
CM364 Copper Age 3500–2000 CC
CM9B Copper Age 3500–2000 CC
DA96B Copper Age 3500–2000 CC
MG104 Middle Bronze Age 1740–1430 GC
TV32032 Middle Bronze Age 1740–1430 GC
TV3831 Middle Bronze Age 1740–1430 CC

TYR, rs1042602, light skin, absence of freckles

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 AC
LC42 Middle Neolithic 4200–3500 CC
LC44 Middle Neolithic 4200–3500 CC
CA122A Copper Age 3500–2000 CC
CM364 Copper Age 3500–2000 CC
CM9B Copper Age 3500–2000 CC
DA96B Copper Age 3500–2000 CC
MG104 Middle Bronze Age 1740–1430 CC
TV32032 Middle Bronze Age 1740–1430 AC
TV3831 Middle Bronze Age 1740–1430 CC

TYR, rs1393350, blond hair, blue eyes

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 GG
LC42 Middle Neolithic 4200–3500 AG
LC44 Middle Neolithic 4200–3500 GG
CA122A Copper Age 3500–2000 GG
CM364 Copper Age 3500–2000 GG
CM9B Copper Age 3500–2000 GG
DA96B Copper Age 3500–2000 GG
MG104 Middle Bronze Age 1740–1430 GG
TV32032 Middle Bronze Age 1740–1430 GG
TV3831 Middle Bronze Age 1740–1430 AG

TYRP1, rs2733831, light hair and eyes

Sample Period Date BC GT
LC41 Middle Neolithic 4200–3500 AA
LC42 Middle Neolithic 4200–3500 GG
LC44 Middle Neolithic 4200–3500 GG
CA122A Copper Age 3500–2000 GG
CM364 Copper Age 3500–2000 GG
CM9B Copper Age 3500–2000 AG
DA96B Copper Age 3500–2000 AG
MG104 Middle Bronze Age 1740–1430 AA
TV32032 Middle Bronze Age 1740–1430 AA
TV3831 Middle Bronze Age 1740–1430 AG
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4 comments on “Phenotype SNPs from prehistoric Portugal
  1. vsva says:

    Can you look also on the y snp calls from portugal?

  2. LukaszM says:

    Hello Genetiker
    Did you during your analysis created .bam files from those fastq which were published on ENA? If so, could you upload them to google drive? I want to convert them to Gedmatch and give people possibility to compare with them.

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