Phenotype SNPs from ancient Egypt

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

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/3
JK2888  Ptolemaic      97–2     0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/1

KITLG, rs12821256, blond hair

Sample  Period         Date BC  D/T
JK2134  Pre-Ptolemaic  776–569  0/1
JK2911  Pre-Ptolemaic  769–560  0/2

MC1R, rs1110400, red hair

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/3
JK2888  Ptolemaic      97–2     0/6

MC1R, rs11547464, red hair

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/2
JK2888  Ptolemaic      97–2     0/3

MC1R, rs1805005, blond hair, fair skin

Sample  Period     Date BC  D/T
JK2888  Ptolemaic  97–2     0/1

MC1R, rs1805006, red hair, fair skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/4

MC1R, rs1805007, red hair, fair skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  1/4
JK2888  Ptolemaic      97–2     0/5

MC1R, rs1805008, red hair, fair skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/3
JK2888  Ptolemaic      97–2     0/1

MC1R, rs1805009, red hair, fair skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/3
JK2888  Ptolemaic      97–2     0/1

MCM6, rs4988235, ability to digest milk

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/10

OCA2/HERC2, rs12913832, blue eyes

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/2

SLC24A5, rs1426654, Caucasoid light skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  2/2
JK2888  Ptolemaic      97–2     1/1

SLC45A2, rs16891982, Caucasoid light skin

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/7

TYR, rs1042602, light skin, absence of freckles

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/4
JK2888  Ptolemaic      97–2     1/1

TYR, rs1393350, blond hair, blue eyes

Sample  Period         Date BC  D/T
JK2911  Pre-Ptolemaic  769–560  0/2
JK2888  Ptolemaic      97–2     0/2
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2 comments on “Phenotype SNPs from ancient Egypt
  1. Griffon says:

    https://genetiker.wordpress.com/2017/04/01/k-14-admixture-analysis-of-neolithic-estonian-genomes/

    Hello, this admixture chart in the link above is nice because it separates navy blue WHG and dark blue EHG components from each other and it’s also good that it shows that CHG is basically mostly admixed Neolithic Iran but I’ve a few suggestions. I wonder why papuan cluster and australoid ancestry inside that green cluster are separate in the first place. Are types of australoid ancestry in them so divergent it can’t be assimilated by the purple cluster? Could you try to separate that green Veddoid+Iran/CHG component because it’s quite cryptic why South Asians have this mysterious mixed component and separate Papuan and Iran N components. Maybe if you add Onge, Paniya and Paliyar samples it will form separate clusters. Or you can try to separate them with fineStructure. Papuan/Australian and Onge/ASI should have separate components. Also could you add Iron Gates hunter gatherers from Balkans, Varna HGs, Ancient Egyptians and more named farmer samples such as Boncuklu, Tepecik-Ciftlik, Gokhem, Barcin, Kumtepe, Menteşe, P192-1 and those new Peloponnese farmer samples. I know you’ve some farmers but most aren’t named so I don’t know which is which. Last important addition would be Devil’s Gate Hunter Gatherers and Lake Baikal Hunter Gatherers. I wonder how these two ancient East Asians would compare to modern with your admixture.

  2. Griffon says:

    I also noticed that you are missing other important Near Eastern samples that would allow visualizing genetic changes in the Middle East over time namely NE farmers(NE1, NE3 etc), Anatolia Chalcolithic, Jordan EBA, Sidon BA, Armenia EBA. Also Baltic BA. Even if it won’t form another cluster Paniya and Onge are worth to add as they are closest to the ASI from moderns.

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