Phenotype SNPs from Neolithic central Asia Minor

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for Neolithic genomes from central Asia Minor. 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                 Date BC    D/T
Bon004  Pre-Pottery Neolithic  > 8300     1/1
Bon002  Pre-Pottery Neolithic  8279–7977  5/5

ASIP, rs6058017, Veddoid brown skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  4/4

EDAR, rs3827760, Mongoloid teeth, hair, etc.

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/2
Tep002  Pottery Neolithic      7500–5800  0/1
Tep003  Pottery Neolithic      7500–5800  0/2
Tep004  Pottery Neolithic      7500–5800  0/1
Tep006  Pottery Neolithic      7500–5800  0/1

IRF4, rs12203592, light hair and eyes, freckling

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/1

KITLG, rs12821256, blond hair

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/1
Tep003  Pottery Neolithic      7500–5800  0/1
Tep004  Pottery Neolithic      7500–5800  0/1

KITLG, rs642742, Veddoid brown skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  10/11
Tep004  Pottery Neolithic      7500–5800  1/1
Tep006  Pottery Neolithic      7500–5800  1/1

MC1R, rs1110400, red hair

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/3
Tep003  Pottery Neolithic      7500–5800  0/2

MC1R, rs11547464, red hair

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/6
Tep004  Pottery Neolithic      7500–5800  0/1

MC1R, rs1805005, blond hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/7

MC1R, rs1805006, red hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/4
Tep003  Pottery Neolithic      7500–5800  0/2

MC1R, rs1805007, red hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/2
Tep003  Pottery Neolithic      7500–5800  0/1
Tep004  Pottery Neolithic      7500–5800  0/1

MC1R, rs1805008, red hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/5
Tep003  Pottery Neolithic      7500–5800  0/1

MC1R, rs1805009, red hair, fair skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/6
Tep003  Pottery Neolithic      7500–5800  0/2

MCM6, rs182549, ability to digest milk

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/26
Tep003  Pottery Neolithic      7500–5800  0/3

MCM6, rs4988235, ability to digest milk

Sample  Period             Date BC    D/T
Tep002  Pottery Neolithic  7500–5800  0/1
Tep003  Pottery Neolithic  7500–5800  1/4

OCA2, rs1800407, green or hazel eyes

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  1/8
Tep003  Pottery Neolithic      7500–5800  0/1

OCA2, rs1800414, Mongoloid light skin

Sample  Period                 Date BC    D/T
Bon004  Pre-Pottery Neolithic  > 8300     0/1
Bon002  Pre-Pottery Neolithic  8279–7977  0/12
Tep002  Pottery Neolithic      7500–5800  0/1

OCA2/HERC2, rs12913832, blue eyes

Sample  Period                 Date BC    D/T
Bon004  Pre-Pottery Neolithic  > 8300     0/1
Bon002  Pre-Pottery Neolithic  8279–7977  1/6
Tep002  Pottery Neolithic      7500–5800  0/1
Tep003  Pottery Neolithic      7500–5800  0/1

SLC24A5, rs1426654, Caucasoid light skin

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  2/3

SLC45A2, rs16891982, Caucasoid light skin

Sample  Period             Date BC    D/T
Tep006  Pottery Neolithic  7500–5800  1/1

TYR, rs1042602, light skin, absence of freckles

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/3
Tep003  Pottery Neolithic      7500–5800  0/2
Tep004  Pottery Neolithic      7500–5800  0/1

TYR, rs1393350, blond hair, blue eyes

Sample  Period                 Date BC    D/T
Bon002  Pre-Pottery Neolithic  8279–7977  0/10

TYRP1, rs2733831, light hair and eyes

Sample  Period                 Date BC    D/T
Bon005  Pre-Pottery Neolithic  8300–8240  0/1
Bon002  Pre-Pottery Neolithic  8279–7977  2/3
Tep002  Pottery Neolithic      7500–5800  1/2
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21 comments on “Phenotype SNPs from Neolithic central Asia Minor
  1. Bob O'Moler says:

    Hi Genetiker. I went through all of your articles and noticed there are no phenotype SNP calls for some ancient genomes like Bichon, Kotias, Satsurblia, Loschbour, Stuttgart, Otzi and Saqqaq. It’s a shame because most of these are high coverage genomes. Could you possibly do them? You could also add some older samples like Ust-Ishim and Kostenki, and add allele counts for Anzick, Kennewick Man, Mal’ta and Afontova Gora 2. Keep up the good work!

    • Anon says:

      Phenotype SNPs for the Hinxton samples would be nice too. I suspect the Anglo-Saxon ones should be the lightest of any ancient samples thus far, and it’d be nice to see how they compared with the indigenous Brit ones.

      It’d also be very useful if you would do one for a modern genome of a person that’s known to have say blonde hair so we see how it actually looks in terms of these SNPs.

  2. Genetiker says:

    Bichon:

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               9/9
    ASIP        rs6058017   Veddoid brown skin               11/11
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      0/16
    IRF4        rs12203592  light hair and eyes, freckling   0/13
    KITLG       rs12821256  blond hair                       0/8
    KITLG       rs642742    Veddoid brown skin               4/7
    MC1R        rs1110400   red hair                         0/13
    MC1R        rs11547464  red hair                         0/16
    MC1R        rs1805005   blond hair, fair skin            0/10
    MC1R        rs1805006   red hair, fair skin              0/10
    MC1R        rs1805007   red hair, fair skin              0/17
    MC1R        rs1805008   red hair, fair skin              0/15
    MC1R        rs1805009   red hair, fair skin              0/11
    MCM6        rs182549    ability to digest milk           0/9
    MCM6        rs4988235   ability to digest milk           0/11
    OCA2        rs1800407   green or hazel eyes              0/11
    OCA2        rs1800414   Mongoloid light skin             0/7
    OCA2/HERC2  rs12913832  blue eyes                        3/9
    SLC24A5     rs1426654   Caucasoid light skin             0/25
    SLC45A2     rs16891982  Caucasoid light skin             0/4
    TYR         rs1042602   light skin, absence of freckles  0/11
    TYR         rs1393350   blond hair, blue eyes            0/14
    TYRP1       rs2733831   light hair and eyes              4/9
  3. Genetiker says:

    Kotias:

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               15/15
    ASIP        rs6058017   Veddoid brown skin               5/5
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      0/20
    IRF4        rs12203592  light hair and eyes, freckling   0/19
    KITLG       rs12821256  blond hair                       0/11
    KITLG       rs642742    Veddoid brown skin               15/15
    MC1R        rs1110400   red hair                         0/16
    MC1R        rs11547464  red hair                         0/27
    MC1R        rs1805005   blond hair, fair skin            0/9
    MC1R        rs1805006   red hair, fair skin              0/14
    MC1R        rs1805007   red hair, fair skin              0/22
    MC1R        rs1805008   red hair, fair skin              0/14
    MC1R        rs1805009   red hair, fair skin              0/19
    MCM6        rs182549    ability to digest milk           0/10
    MCM6        rs4988235   ability to digest milk           0/16
    OCA2        rs1800407   green or hazel eyes              0/8
    OCA2        rs1800414   Mongoloid light skin             0/15
    OCA2/HERC2  rs12913832  blue eyes                        0/15
    SLC24A5     rs1426654   Caucasoid light skin             13/13
    SLC45A2     rs16891982  Caucasoid light skin             0/21
    TYR         rs1042602   light skin, absence of freckles  0/19
    TYR         rs1393350   blond hair, blue eyes            0/14
    TYRP1       rs2733831   light hair and eyes              13/13
  4. Genetiker says:

    Satsurblia:

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               2/2
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      0/1
    IRF4        rs12203592  light hair and eyes, freckling   0/7
    KITLG       rs12821256  blond hair                       0/2
    KITLG       rs642742    Veddoid brown skin               1/1
    MC1R        rs11547464  red hair                         0/1
    MC1R        rs1805005   blond hair, fair skin            0/1
    MC1R        rs1805006   red hair, fair skin              0/1
    MC1R        rs1805009   red hair, fair skin              0/1
    MCM6        rs4988235   ability to digest milk           0/1
    OCA2        rs1800407   green or hazel eyes              0/1
    OCA2        rs1800414   Mongoloid light skin             0/2
    OCA2/HERC2  rs12913832  blue eyes                        2/3
    SLC24A5     rs1426654   Caucasoid light skin             4/4
    SLC45A2     rs16891982  Caucasoid light skin             0/2
    TYR         rs1042602   light skin, absence of freckles  0/2
    TYR         rs1393350   blond hair, blue eyes            0/1
    TYRP1       rs2733831   light hair and eyes              1/1
  5. Genetiker says:

    Loschbour:

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               7/7
    ASIP        rs6058017   Veddoid brown skin               6/6
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      0/17
    IRF4        rs12203592  light hair and eyes, freckling   21/21
    KITLG       rs12821256  blond hair                       0/16
    KITLG       rs642742    Veddoid brown skin               16/36
    MC1R        rs1110400   red hair                         0/16
    MC1R        rs11547464  red hair                         0/15
    MC1R        rs1805005   blond hair, fair skin            0/11
    MC1R        rs1805006   red hair, fair skin              0/11
    MC1R        rs1805007   red hair, fair skin              0/14
    MC1R        rs1805008   red hair, fair skin              0/16
    MC1R        rs1805009   red hair, fair skin              0/14
    MCM6        rs182549    ability to digest milk           1/29
    MCM6        rs4988235   ability to digest milk           0/19
    OCA2        rs1800407   green or hazel eyes              0/16
    OCA2        rs1800414   Mongoloid light skin             0/20
    OCA2/HERC2  rs12913832  blue eyes                        21/21
    SLC24A5     rs1426654   Caucasoid light skin             0/20
    SLC45A2     rs16891982  Caucasoid light skin             0/18
    TYR         rs1042602   light skin, absence of freckles  0/17
    TYR         rs1393350   blond hair, blue eyes            0/30
    TYRP1       rs2733831   light hair and eyes              26/26
    • Anon says:

      When his genome was released why was he widely described as “blue eyes, dark skin, black hair” when he’s fully derived for IRF4 and TYRP1? Pigment adding SNPs that aren’t accounted for here maybe?

      According to this, Loshbour, Villabruna had light hair and La Brana/KO1 didn’t. That’s 50/50 rather than the mainstream narrative of fully dark WHGs.

      Still hoping you’ll do some of the Hinxton samples.

  6. Genetiker says:

    Stuttgart:

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               16/16
    ASIP        rs6058017   Veddoid brown skin               10/10
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      0/29
    IRF4        rs12203592  light hair and eyes, freckling   0/25
    KITLG       rs12821256  blond hair                       0/18
    KITLG       rs642742    Veddoid brown skin               33/33
    MC1R        rs1110400   red hair                         0/33
    MC1R        rs11547464  red hair                         1/29
    MC1R        rs1805005   blond hair, fair skin            0/19
    MC1R        rs1805006   red hair, fair skin              0/21
    MC1R        rs1805007   red hair, fair skin              0/34
    MC1R        rs1805008   red hair, fair skin              1/30
    MC1R        rs1805009   red hair, fair skin              0/27
    MCM6        rs182549    ability to digest milk           0/29
    MCM6        rs4988235   ability to digest milk           0/25
    OCA2        rs1800407   green or hazel eyes              0/9
    OCA2        rs1800414   Mongoloid light skin             0/15
    OCA2/HERC2  rs12913832  blue eyes                        0/21
    SLC24A5     rs1426654   Caucasoid light skin             14/14
    SLC45A2     rs16891982  Caucasoid light skin             0/21
    TYR         rs1042602   light skin, absence of freckles  11/14
    TYR         rs1393350   blond hair, blue eyes            0/16
    TYRP1       rs2733831   light hair and eyes              17/17
  7. Bob O'Moler says:

    Thanks a lot Genetiker. I forgot to mention Oase and Tianyuan, it would be nice to see their phenotype SNPs too. One question about Y-DNA, how reliable are Z4842 calls for Ust-Ishim and Oase (derived/total alelle count)?

  8. Genetiker says:

    Ust’-Ishim:

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               35/35
    ASIP        rs6058017   Veddoid brown skin               24/24
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      0/42
    IRF4        rs12203592  light hair and eyes, freckling   0/38
    KITLG       rs12821256  blond hair                       0/38
    KITLG       rs642742    Veddoid brown skin               23/48
    MC1R        rs1110400   red hair                         0/37
    MC1R        rs11547464  red hair                         0/23
    MC1R        rs1805005   blond hair, fair skin            0/22
    MC1R        rs1805006   red hair, fair skin              0/29
    MC1R        rs1805007   red hair, fair skin              0/32
    MC1R        rs1805008   red hair, fair skin              0/32
    MC1R        rs1805009   red hair, fair skin              0/25
    MCM6        rs182549    ability to digest milk           2/41
    MCM6        rs4988235   ability to digest milk           0/31
    OCA2        rs1800407   green or hazel eyes              0/25
    OCA2        rs1800414   Mongoloid light skin             0/62
    OCA2/HERC2  rs12913832  blue eyes                        0/50
    SLC24A5     rs1426654   Caucasoid light skin             1/52
    SLC45A2     rs16891982  Caucasoid light skin             0/46
    TYR         rs1042602   light skin, absence of freckles  0/34
    TYR         rs1393350   blond hair, blue eyes            0/54
    TYRP1       rs2733831   light hair and eyes              0/60
  9. Genetiker says:

    Anzick 1:

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               52/52
    ASIP        rs6058017   Veddoid brown skin               38/38
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      18/38
    IRF4        rs12203592  light hair and eyes, freckling   0/18
    KITLG       rs12821256  blond hair                       0/15
    KITLG       rs642742    Veddoid brown skin               6/6
    MC1R        rs1110400   red hair                         0/54
    MC1R        rs11547464  red hair                         1/70
    MC1R        rs1805005   blond hair, fair skin            0/53
    MC1R        rs1805006   red hair, fair skin              0/57
    MC1R        rs1805007   red hair, fair skin              0/55
    MC1R        rs1805008   red hair, fair skin              1/74
    MC1R        rs1805009   red hair, fair skin              0/40
    MCM6        rs182549    ability to digest milk           0/44
    MCM6        rs4988235   ability to digest milk           0/19
    OCA2        rs1800407   green or hazel eyes              1/68
    OCA2        rs1800414   Mongoloid light skin             0/27
    OCA2/HERC2  rs12913832  blue eyes                        0/30
    SLC24A5     rs1426654   Caucasoid light skin             1/28
    SLC45A2     rs16891982  Caucasoid light skin             0/23
    TYR         rs1042602   light skin, absence of freckles  0/19
    TYR         rs1393350   blond hair, blue eyes            0/18
    TYRP1       rs2733831   light hair and eyes              3/7
  10. Genetiker says:

    Kennewick Man:

    Gene        SNP         Phenotype                       D/T
    ASIP        rs6058017   Veddoid brown skin              1/1
    EDAR        rs3827760   Mongoloid teeth, hair, etc.     1/1
    IRF4        rs12203592  light hair and eyes, freckling  0/4
    KITLG       rs642742    Veddoid brown skin              1/1
    MC1R        rs11547464  red hair                        0/1
    MC1R        rs1805005   blond hair, fair skin           0/1
    MC1R        rs1805007   red hair, fair skin             0/1
    MCM6        rs4988235   ability to digest milk          1/1
    OCA2        rs1800407   green or hazel eyes             0/1
    OCA2        rs1800414   Mongoloid light skin            0/1
    OCA2/HERC2  rs12913832  blue eyes                       0/3
    SLC24A5     rs1426654   Caucasoid light skin            0/2
    TYR         rs1393350   blond hair, blue eyes           0/4
    TYRP1       rs2733831   light hair and eyes             0/2
  11. Genetiker says:

    Mal’ta 1:

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               3/3
    ASIP        rs6058017   Veddoid brown skin               1/1
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      0/2
    IRF4        rs12203592  light hair and eyes, freckling   0/3
    KITLG       rs642742    Veddoid brown skin               1/1
    MC1R        rs1110400   red hair                         0/1
    MC1R        rs11547464  red hair                         0/1
    MC1R        rs1805005   blond hair, fair skin            0/3
    MC1R        rs1805006   red hair, fair skin              0/3
    MC1R        rs1805007   red hair, fair skin              0/1
    MC1R        rs1805009   red hair, fair skin              0/0
    MCM6        rs4988235   ability to digest milk           0/1
    OCA2        rs1800407   green or hazel eyes              0/5
    OCA2        rs1800414   Mongoloid light skin             0/3
    OCA2/HERC2  rs12913832  blue eyes                        0/2
    SLC24A5     rs1426654   Caucasoid light skin             0/2
    TYR         rs1042602   light skin, absence of freckles  0/2
    TYRP1       rs2733831   light hair and eyes              0/1
  12. Genetiker says:

    Afontova Gora 2:

    Gene     SNP        Phenotype             D/T
    ASIP     rs2424984  Veddoid brown skin    1/1
    OCA2     rs1800407  green or hazel eyes   0/1
    SLC24A5  rs1426654  Caucasoid light skin  1/1
    TYRP1    rs2733831  light hair and eyes   0/1
  13. Genetiker says:

    Oase 1:

    Gene     SNP         Phenotype                        D/T
    EDAR     rs3827760   Mongoloid teeth, hair, etc.      0/1
    MC1R     rs1110400   red hair                         0/2
    MC1R     rs11547464  red hair                         0/1
    MC1R     rs1805005   blond hair, fair skin            0/3
    MC1R     rs1805006   red hair, fair skin              0/1
    MC1R     rs1805007   red hair, fair skin              0/3
    MC1R     rs1805008   red hair, fair skin              0/2
    MC1R     rs1805009   red hair, fair skin              0/4
    MCM6     rs4988235   ability to digest milk           0/1
    SLC45A2  rs16891982  Caucasoid light skin             0/3
    TYR      rs1042602   light skin, absence of freckles  0/1
    TYR      rs1393350   blond hair, blue eyes            0/1
  14. Genetiker says:

    Below are the phenotype SNPs for Kostenki 14. He did indeed have one copy of the rs1805007 red hair mutation.

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               1/1
    ASIP        rs6058017   Veddoid brown skin               2/2
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      0/47
    IRF4        rs12203592  light hair and eyes, freckling   1/43
    KITLG       rs12821256  blond hair                       0/58
    KITLG       rs642742    Veddoid brown skin               0/6
    MC1R        rs1110400   red hair                         2/140
    MC1R        rs11547464  red hair                         0/113
    MC1R        rs1805005   blond hair, fair skin            1/37
    MC1R        rs1805006   red hair, fair skin              1/81
    MC1R        rs1805007   red hair, fair skin              60/143
    MC1R        rs1805008   red hair, fair skin              2/104
    MC1R        rs1805009   red hair, fair skin              0/207
    MCM6        rs182549    ability to digest milk           0/25
    MCM6        rs4988235   ability to digest milk           0/140
    OCA2        rs1800407   green or hazel eyes              1/47
    OCA2        rs1800414   Mongoloid light skin             0/64
    OCA2/HERC2  rs12913832  blue eyes                        0/54
    SLC24A5     rs1426654   Caucasoid light skin             1/6
    SLC45A2     rs16891982  Caucasoid light skin             2/113
    TYR         rs1042602   light skin, absence of freckles  0/107
    TYR         rs1393350   blond hair, blue eyes            0/140
  15. Genetiker says:

    Ötzi:

    Gene        SNP         Phenotype                        D/T
    ASIP        rs2424984   Veddoid brown skin               12/12
    ASIP        rs6058017   Veddoid brown skin               5/5
    EDAR        rs3827760   Mongoloid teeth, hair, etc.      0/10
    IRF4        rs12203592  light hair and eyes, freckling   0/2
    KITLG       rs12821256  blond hair                       0/7
    KITLG       rs642742    Veddoid brown skin               1/1
    MC1R        rs1110400   red hair                         0/5
    MC1R        rs11547464  red hair                         0/10
    MC1R        rs1805005   blond hair, fair skin            0/1
    MC1R        rs1805006   red hair, fair skin              0/9
    MC1R        rs1805007   red hair, fair skin              0/7
    MC1R        rs1805008   red hair, fair skin              0/1
    MC1R        rs1805009   red hair, fair skin              0/5
    MCM6        rs182549    ability to digest milk           0/10
    MCM6        rs4988235   ability to digest milk           0/8
    OCA2        rs1800407   green or hazel eyes              0/6
    OCA2        rs1800414   Mongoloid light skin             0/23
    OCA2/HERC2  rs12913832  blue eyes                        0/16
    SLC24A5     rs1426654   Caucasoid light skin             15/15
    SLC45A2     rs16891982  Caucasoid light skin             10/10
    TYR         rs1042602   light skin, absence of freckles  1/13
    TYR         rs1393350   blond hair, blue eyes            0/5

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