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четверг, 5 мая 2016 г.

Phenotype SNPs from Ice Age Europe

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for 37 genomes from Ice Age Europe. 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        Country  Years BP       Culture        D/T
Goyet Q116-1  Belgium  35,160–34,430  Aurignacian    0/1
Villabruna    Italy    14,180–13,780  Epigravettian  1/1
ASIP, rs6058017, Veddoid brown skin
Sample           Country  Years BP       Culture      D/T
Afontova Gora 3  Russia   16,930–16,490  Unassigned   1/1
Goyet Q-2        Belgium  15,230–14,780  Magdalenian  1/1
EDAR, rs3827760, Mongoloid teeth, hair, etc.
Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/10
Paglicci 133     Italy    34,580–31,210  Gravettian      0/1
Krems WA3        Austria  31,250–30,690  Gravettian      0/1
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/4
Goyet Q53-1      Belgium  28,230–27,720  Gravettian      0/1
Ostuni 1         Italy    27,810–27,430  Gravettian      0/2
El Mirón         Spain    18,830–18,610  Magdalenian     0/8
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Goyet Q-2        Belgium  15,230–14,780  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   0/20
Iboussières 39   France   12,040–11,410  Epipaleolithic  0/1
Ranchot 88       France   10,240–9,930   Mesolithic      0/2
Berry-au-Bac     France   7,320–7,170    Mesolithic      0/1
IRF4, rs12203592, light hair and eyes, freckling
Sample           Country  Years BP       Culture         D/T
Muierii 2        Romania  33,760–32,840  Unassigned      0/1
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/3
Ostuni 1         Italy    27,810–27,430  Gravettian      0/3
El Mirón         Spain    18,830–18,610  Magdalenian     0/3
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Villabruna       Italy    14,180–13,780  Epigravettian   10/10
Rochedane        France   13,090–12,830  Epipaleolithic  0/1
KITLG, rs12821256, blond hair
Sample         Country  Years BP       Culture         D/T
Goyet Q116-1   Belgium  35,160–34,430  Aurignacian     0/2
Pavlov 1       Czechia  31,110–29,410  Gravettian      0/1
Věstonice 16   Czechia  30,710–29,310  Gravettian      0/2
Ostuni 1       Italy    27,810–27,430  Gravettian      0/1
Hohle Fels 49  Germany  16,000–14,260  Magdalenian     0/1
Villabruna     Italy    14,180–13,780  Epigravettian   0/10
Rochedane      France   13,090–12,830  Epipaleolithic  0/1
KITLG, rs642742, Veddoid brown skin
Sample        Country  Years BP       Culture      D/T
Goyet Q116-1  Belgium  35,160–34,430  Aurignacian  1/1
MC1R, rs1110400, red hair
Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/11
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/2
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/28
Ostuni 1         Italy    27,810–27,430  Gravettian      0/6
El Mirón         Spain    18,830–18,610  Magdalenian     0/31
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/2
Hohle Fels 79    Germany  15,070–14,270  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   0/33
Rochedane        France   13,090–12,830  Epipaleolithic  0/2
Falkenstein      Germany  9,410–8,990    Mesolithic      0/2
Bockstein        Germany  8,370–8,160    Mesolithic      0/1
MC1R, rs11547464, red hair
Sample        Country  Years BP       Culture         D/T
Goyet Q116-1  Belgium  35,160–34,430  Aurignacian     0/9
Muierii 2     Romania  33,760–32,840  Unassigned      0/1
Věstonice 13  Czechia  31,070–30,670  Gravettian      0/1
Pavlov 1      Czechia  31,110–29,410  Gravettian      0/1
Věstonice 43  Czechia  30,710–29,310  Gravettian      0/4
Věstonice 16  Czechia  30,710–29,310  Gravettian      0/12
Ostuni 1      Italy    27,810–27,430  Gravettian      0/3
Goyet Q56-16  Belgium  26,600–26,040  Gravettian      1/1
El Mirón      Spain    18,830–18,610  Magdalenian     1/20
Villabruna    Italy    14,180–13,780  Epigravettian   0/15
Rochedane     France   13,090–12,830  Epipaleolithic  0/1
Ranchot 88    France   10,240–9,930   Mesolithic      0/1
Falkenstein   Germany  9,410–8,990    Mesolithic      0/1
MC1R, rs1805005, blond hair, fair skin
Sample           Country  Years BP       Culture        D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian    0/2
Věstonice 16     Czechia  30,710–29,310  Gravettian     0/4
Ostuni 1         Italy    27,810–27,430  Gravettian     0/2
El Mirón         Spain    18,830–18,610  Magdalenian    0/3
Afontova Gora 3  Russia   16,930–16,490  Unassigned     0/3
Villabruna       Italy    14,180–13,780  Epigravettian  0/11
Ranchot 88       France   10,240–9,930   Mesolithic     0/1
Falkenstein      Germany  9,410–8,990    Mesolithic     0/1
MC1R, rs1805006, red hair, fair skin
Sample         Country  Years BP       Culture        D/T
Goyet Q116-1   Belgium  35,160–34,430  Aurignacian    0/3
Věstonice 13   Czechia  31,070–30,670  Gravettian     0/2
Věstonice 16   Czechia  30,710–29,310  Gravettian     0/10
Ostuni 1       Italy    27,810–27,430  Gravettian     0/1
El Mirón       Spain    18,830–18,610  Magdalenian    0/14
Hohle Fels 49  Germany  16,000–14,260  Magdalenian    0/2
Villabruna     Italy    14,180–13,780  Epigravettian  0/24
Ranchot 88     France   10,240–9,930   Mesolithic     0/2
Falkenstein    Germany  9,410–8,990    Mesolithic     0/1
Bockstein      Germany  8,370–8,160    Mesolithic     0/2
Berry-au-Bac   France   7,320–7,170    Mesolithic     0/1
MC1R, rs1805007, red hair, fair skin
Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/11
Pavlov 1         Czechia  31,110–29,410  Gravettian      0/1
Věstonice 43     Czechia  30,710–29,310  Gravettian      1/5
Věstonice 16     Czechia  30,710–29,310  Gravettian      1/27
Ostuni 1         Italy    27,810–27,430  Gravettian      0/4
El Mirón         Spain    18,830–18,610  Magdalenian     0/33
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Hohle Fels 79    Germany  15,070–14,270  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   2/32
Rochedane        France   13,090–12,830  Epipaleolithic  0/2
Falkenstein      Germany  9,410–8,990    Mesolithic      0/1
MC1R, rs1805008, red hair, fair skin
Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/8
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/2
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/21
Ostuni 1         Italy    27,810–27,430  Gravettian      0/4
El Mirón         Spain    18,830–18,610  Magdalenian     0/17
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/2
Goyet Q-2        Belgium  15,230–14,780  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   2/25
Rochedane        France   13,090–12,830  Epipaleolithic  0/1
Falkenstein      Germany  9,410–8,990    Mesolithic      0/4
Bockstein        Germany  8,370–8,160    Mesolithic      0/1
MC1R, rs1805009, red hair, fair skin
Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/9
Paglicci 133     Italy    34,580–31,210  Gravettian      0/1
Věstonice 13     Czechia  31,070–30,670  Gravettian      0/2
Věstonice 14     Czechia  31,070–30,670  Gravettian      0/1
Věstonice 43     Czechia  30,710–29,310  Gravettian      0/3
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/27
Ostuni 1         Italy    27,810–27,430  Gravettian      0/5
El Mirón         Spain    18,830–18,610  Magdalenian     0/34
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Hohle Fels 49    Germany  16,000–14,260  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   0/32
Rochedane        France   13,090–12,830  Epipaleolithic  0/1
Ranchot 88       France   10,240–9,930   Mesolithic      0/3
MCM6, rs182549, ability to digest milk
Sample        Country  Years BP       Culture        D/T
Goyet Q116-1  Belgium  35,160–34,430  Aurignacian    0/1
Věstonice 15  Czechia  31,070–30,670  Gravettian     1/1
El Mirón      Spain    18,830–18,610  Magdalenian    0/2
Villabruna    Italy    14,180–13,780  Epigravettian  0/1
Ranchot 88    France   10,240–9,930   Mesolithic     0/1
Bockstein     Germany  8,370–8,160    Mesolithic     0/1
MCM6, rs4988235, ability to digest milk
Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/8
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/13
Ostuni 2         Italy    29,310–28,640  Gravettian      0/1
Ostuni 1         Italy    27,810–27,430  Gravettian      0/1
El Mirón         Spain    18,830–18,610  Magdalenian     0/2
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Burkhardtshöhle  Germany  15,080–14,150  Magdalenian     0/2
Villabruna       Italy    14,180–13,780  Epigravettian   0/17
Rochedane        France   13,090–12,830  Epipaleolithic  0/1
Ranchot 88       France   10,240–9,930   Mesolithic      0/2
Les Closeaux 13  France   10,240–9,560   Mesolithic      0/1
Berry-au-Bac     France   7,320–7,170    Mesolithic      0/1
OCA2, rs1800407, green or hazel eyes
Sample         Country  Years BP       Culture         D/T
Goyet Q116-1   Belgium  35,160–34,430  Aurignacian     0/7
Muierii 2      Romania  33,760–32,840  Unassigned      0/2
Paglicci 133   Italy    34,580–31,210  Gravettian      0/1
Věstonice 43   Czechia  30,710–29,310  Gravettian      0/1
Věstonice 16   Czechia  30,710–29,310  Gravettian      0/10
Ostuni 1       Italy    27,810–27,430  Gravettian      0/2
El Mirón       Spain    18,830–18,610  Magdalenian     0/5
Hohle Fels 79  Germany  15,070–14,270  Magdalenian     0/1
Villabruna     Italy    14,180–13,780  Epigravettian   1/21
Rochedane      France   13,090–12,830  Epipaleolithic  0/1
Ranchot 88     France   10,240–9,930   Mesolithic      0/1
Falkenstein    Germany  9,410–8,990    Mesolithic      0/1
OCA2, rs1800414, Mongoloid light skin
Sample           Country  Years BP       Culture         D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian     0/1
Muierii 2        Romania  33,760–32,840  Unassigned      0/1
Pavlov 1         Czechia  31,110–29,410  Gravettian      0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian      0/2
El Mirón         Spain    18,830–18,610  Magdalenian     0/3
Afontova Gora 3  Russia   16,930–16,490  Unassigned      0/1
Hohle Fels 49    Germany  16,000–14,260  Magdalenian     0/1
Villabruna       Italy    14,180–13,780  Epigravettian   0/12
Rochedane        France   13,090–12,830  Epipaleolithic  0/2
Chaudardes 1     France   8,360–8,050    Mesolithic      0/1
OCA2/HERC2, rs12913832, blue eyes
Sample           Country  Years BP       Culture        D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian    0/1
Kostenki 12      Russia   32,990–31,840  Unassigned     0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian     0/5
Ostuni 1         Italy    27,810–27,430  Gravettian     0/2
El Mirón         Spain    18,830–18,610  Magdalenian    0/5
Afontova Gora 3  Russia   16,930–16,490  Unassigned     0/1
Goyet Q-2        Belgium  15,230–14,780  Magdalenian    0/1
Villabruna       Italy    14,180–13,780  Epigravettian  11/11
Ranchot 88       France   10,240–9,930   Mesolithic     1/1
Falkenstein      Germany  9,410–8,990    Mesolithic     1/1
SLC24A5, rs1426654, Caucasoid light skin
Sample      Country  Years BP       Culture        D/T
Ostuni 1    Italy    27,810–27,430  Gravettian     0/1
El Mirón    Spain    18,830–18,610  Magdalenian    0/1
Villabruna  Italy    14,180–13,780  Epigravettian  0/5
Ranchot 88  France   10,240–9,930   Mesolithic     0/1
SLC45A2, rs16891982, Caucasoid light skin
Sample           Country  Years BP       Culture        D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian    0/6
Muierii 2        Romania  33,760–32,840  Unassigned     0/1
Věstonice 13     Czechia  31,070–30,670  Gravettian     0/1
Věstonice 16     Czechia  30,710–29,310  Gravettian     1/18
El Mirón         Spain    18,830–18,610  Magdalenian    0/11
Afontova Gora 3  Russia   16,930–16,490  Unassigned     0/2
Villabruna       Italy    14,180–13,780  Epigravettian  0/54
Ranchot 88       France   10,240–9,930   Mesolithic     0/3
TYR, rs1042602, light skin, absence of freckles
Sample           Country  Years BP       Culture        D/T
Goyet Q116-1     Belgium  35,160–34,430  Aurignacian    0/5
Věstonice 43     Czechia  30,710–29,310  Gravettian     0/2
Věstonice 16     Czechia  30,710–29,310  Gravettian     0/16
Ostuni 1         Italy    27,810–27,430  Gravettian     0/4
El Mirón         Spain    18,830–18,610  Magdalenian    0/8
Afontova Gora 3  Russia   16,930–16,490  Unassigned     0/1
Brillenhöhle     Germany  15,120–14,440  Magdalenian    0/2
Villabruna       Italy    14,180–13,780  Epigravettian  0/29
Ranchot 88       France   10,240–9,930   Mesolithic     0/3
TYR, rs1393350, blond hair, blue eyes
Sample         Country  Years BP       Culture         D/T
Goyet Q116-1   Belgium  35,160–34,430  Aurignacian     0/2
Muierii 2      Romania  33,760–32,840  Unassigned      0/1
Věstonice 43   Czechia  30,710–29,310  Gravettian      0/1
Věstonice 16   Czechia  30,710–29,310  Gravettian      0/12
Ostuni 1       Italy    27,810–27,430  Gravettian      0/2
El Mirón       Spain    18,830–18,610  Magdalenian     0/9
Hohle Fels 49  Germany  16,000–14,260  Magdalenian     0/1
Villabruna     Italy    14,180–13,780  Epigravettian   0/35
Rochedane      France   13,090–12,830  Epipaleolithic  0/2
Ranchot 88     France   10,240–9,930   Mesolithic      0/2
Falkenstein    Germany  9,410–8,990    Mesolithic      0/1