Fire Haired
04-22-2014, 05:43 AM
This thread is meant to be a reference for pigmentation(SNPs and their alleles) of Mesolithic European hunter gatherers: Loschbour(Luxembourg, 6,000BC), La Brana-1(Spain, 5960-5750 BC), Motala12(Swede, 6,000BC), and also Neolithic European farmer Stuttgart(Germany, 5100-4800 BC). The percentages for Africa, Asia,a nd Europe are actulley the percentages of whatever allele La Brana-1 has. If La Brana-1 had C/C alleles, it shows the percentage of Europeans(northern and western), Africans, and Asians have C/A or C/C. If la Brana-1 had T/C, it would show what percentage Africans, Europeans, and Asians have of whatever the derived allele is, so possibly in that situation T/T and T/C.
<tbody>
SNP
Gene
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
Europe
rs1800414
OCA2
T
C
?
T(3x)
?
?
100<t< td=""></t<>
41<t< td=""></t<>
100<t< td=""></t<>
rs1800407
OCA2
C
T
C/C
C(12x)
C/C()1x)
C/C
100<c< td=""></c<>
100<c< td=""></c<>
92<c< td=""></c<>
rs1545397
OCA2
A
T
A/A
A(1x)
?
A/A
97<a< td=""></a<>
8<a< td=""></a<>
92<a< td=""></a<>
rs4424881
APBA2
T
C
?
TC(1x,4x)
?
?
10<c< td=""></c<>
45<c< td=""></c<>
87<c< td=""></c<>
rs6119471
ASIP
G
C
C/C
C(3x)
C/C (3x)
C/C
36<c< td=""></c<>
100<c< td=""></c<>
100<c< td=""></c<>
rs2378249
ASIP/PIGU
A
G
A/A
A(6x)
A/A (1x)
A/A
86<a< td=""></a<>
85<a< td=""></a<>
88<a< td=""></a<>
rs4911442
ASIP
A
G
?
A(1x)
?
?
100<a< td=""></a<>
100<a< td=""></a<>
91<a< td=""></a<>
rs1042602
TYR
C
A
C/C
C(6x)
C/C (3x)
C/A
99<c< td=""></c<>
100<c< td=""></c<>
63<c< td=""></c<>
rs1126809
TYR
G
A
?
G(6x)
?
?
99<g< td=""></g<>
100<g< td=""></g<>
75<g< td=""></g<>
rs1393350
TYR
G
A
G/G
G(6x)
G/G (4x)
G/G
99<g< td=""></g<>
100<g< td=""></g<>
76<g< td=""></g<>
rs10831496
GRM5
G
A
?
G(2x)
?
?
80<g< td=""></g<>
76<g< td=""></g<>
31<g< td=""></g<>
rs683
TYRP1
A
C
A/A
A(1x)
A/A (1x)
A/A
13<a< td=""></a<>
1<a< td=""></a<>
63<a< td=""></a<>
rs2733831
TYRP1
A
G
?
G(3x)
?
?
6<g< td=""></g<>
1<g< td=""></g<>
60<g< td=""></g<>
rs1408799
TYRP1
T
C
?
C(1x)
?
?
22<c< td=""></c<>
1<c< td=""></c<>
66<c< td=""></c<>
rs1407995
DCT
T
C
?
C(1x)
?
?
82<c< td=""></c<>
24<c< td=""></c<>
82<c< td=""></c<>
rs12203592
IRF4
C
T
T/T
CT(1x,2x)
T/T (3x)
C/C
1<t< td=""></t<>
0<t< td=""></t<>
11<t< td=""></t<>
rs12821256
KITLG
T
C
T/T
T(8x)
T/T (3x)
T/T
100<t< td=""></t<>
100<t< td=""></t<>
86<t< td=""></t<>
rs642742
KITLG
T
C
?
?
?
?
?
?
?
rs28777
SLC45A2
C
A
C/A
C(8x)
A/A (4x)
C/C
80<c< td=""></c<>
88<c< td=""></c<>
2<c< td=""></c<>
rs35395
SLC45A2
T
C
?
T(1x
?
?
76<t< td=""></t<>
88<t< td=""></t<>
2<t< td=""></t<>
rs2402130
SLC45A2
G
A
G/A
GA(2x,4x)
A/A (1x)
G/G
41<a< td=""></a<>
93<a< td=""></a<>
77<a< td=""></a<>
rs12896399
SLC45A2
G
T
G/G
?
?
T/T
?
?
?
rs2470102
SLC45A2
G
A
G/G
G(8x)
A/A(5x)
A/A
92<g< td=""></g<>
75<g< td=""></g<>
1<g< td=""></g<>
rs4959270
EXOC2
C
A
A/A
C(7x)
A/A (1x)
C/C
81<c< td=""></c<>
66<c< td=""></c<>
53<c< td=""></c<>
rs1805009
MC1R
G
C
G/G
G(5x)
G/G (4x)
G/G
100<g< td=""></g<>
100<g< td=""></g<>
99<g< td=""></g<>
rs2228479
MC1R
G
A
G/G
G(11x)
G/G (4x
G/G
100<g< td=""></g<>
76<g< td=""></g<>
93<g< td=""></g<>
rs885479
MC1R
G
A
?
G(6x)
?
?
99<g< td=""></g<>
35<g< td=""></g<>
92<g< td=""></g<>
N29insA
MC1R
C
A
C/C
C(10x)
C/C(5x)
C/C
?
?
?
rs11547464
MC1R
G
A
G/G
G(7x
?
G/G
100<g< td=""></g<>
100<g< td=""></g<>
99<g< td=""></g<>
rs885479
MC1R
G
A
G/G
G(6x)
G/G (3x)
G/G
99<g< td=""></g<>
35<g< td=""></g<>
92<g< td=""></g<>
rs1805008
MC1R
C
T
C/C
C(6x)
C/C (2x)
C/C
99<c< td=""></c<>
100<c< td=""></c<>
93<c< td=""></c<>
rs1805005
MC1R
G
T
G/G
G(12x)
G/G (6x)
G/G
99<g< td=""></g<>
100<g< td=""></g<>
89<g< td=""></g<>
rs1805006
MC1R
C
A
C/C
C(11x)
C/C (6x)
C/C
100<c< td=""></c<>
100<c< td=""></c<>
99<c< td=""></c<>
rs1805007
MC1R
C
T
C/C
C(8x)
?
C/C
100<c< td=""></c<>
100<c< td=""></c<>
92<c< td=""></c<>
Y152OCH
MC1R
C
A
C/C
C(7x)
?
C/C
?
?
?
rs1110400
MC1R
T
C
C/C
T(8x)
?
C/C
100<t< td=""></t<>
100<t< td=""></t<>
100<t< td=""></t<>
rs12913832
OCA2-HERC2
A
G
G/G
G(3x)
G/G (1x)
A/A
4<g< td=""></g<>
0<g< td=""></g<>
71<g< td=""></g<>
rs3935591
OCA2-HERC2
T
C
C/C
C(9x)
T/C (7x)
C/C
21<c< td=""></c<>
27<c< td=""></c<>
82<c< td=""></c<>
rs2240203
OCA2-HERC2
C
T
T/T
T(3x)
T/T (5x)
T/T
36<t< td=""></t<>
61<t< td=""></t<>
93<t< td=""></t<>
rs4778241
OCA2-HERC2
A
C
C/C
C(7x)
C/C (5x)
A/C
40<c< td=""></c<>
23<c< td=""></c<>
78<c< td=""></c<>
rs1129038
OCA2-HERC2
C
T
T/T
T(5x)
T/T (3x)
C/C
4<t< td=""></t<>
0<c< td=""></c<>
71<c< td=""></c<>
rs12593929
OCA2-HERC2
G
A
A/A
A(7x)
A/A (2x)
A/A
37<a< td=""></a<>
58<a< td=""></a<>
97<a< td=""></a<>
rs7183877
OCA2-HERC2
C
A
C/C
C(1x)
?
C/C
92<c< td=""></c<>
70<c< td=""></c<>
90<c< td=""></c<>
rs7170852
OCA2-HERC2
T
A
A/A
A(9x)
A/A (7x)
A/A
20<a< td=""></a<>
27<a< td=""></a<>
81<a< td=""></a<>
rs2238289
OCA2-HERC2
A
G
A/A
A(3x)
A/A (3x)
A/A
32<a< td=""></a<>
29<a< td=""></a<>
84<a< td=""></a<>
rs3940272
OCA2-HERC2
T
G
G/G
G(1x)
?
?
21<g< td=""></g<>
27<g< td=""></g<>
81<g< td=""></g<>
rs8028689
OCA2-HERC2
C
T
T/T
T(3x)
T/T (2x)
T/T
59<g< td=""></g<>
61<g< td=""></g<>
93<g< td=""></g<>
rs11631797
OCA2-HERC2
A
G
G/G
G(4x)
?
G/G
18<g< td=""></g<>
26<g< td=""></g<>
80<g< td=""></g<>
rs916977
OCA2-HERC2
T
C
C/C
C(9x
C/C (2x)
C/C
10<c< td=""></c<>
26<c< td=""></c<>
81<c< td=""></c<>
</tbody>
8-Plex SNPs
<tbody>
SNP
Gene
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
Europe
rs1291382
HERC2
?
?
?
G/G
G/G (1x)
A/A
?
?
?
rs1545397
OCA2
A
T
A/A
A(1x)
?
A/A
97<a< td=""></a<>
8<a< td=""></a<>
92<a< td=""></a<>
rs16891982
SLC45A2
C
G
C/C
CC(6x)
?
C/C
?
?
97 G
rs885479
MC1R
G
A
?
G(6x)
?
?
99<g< td=""></g<>
35<g< td=""></g<>
92<g< td=""></g<>
rs1426654
SLC24A5
G
A
G/G
G/G(3x)
A/A (3x)
A/A
?
?
100 A
rs12896399
SLC45A2
G
T
G/G
?
?
T/T
?
?
?
rs6119471
ASIP
G
C
C/C
C(3x)
C/C (3x)
C/C
36<c< td=""></c<>
100<c< td=""></c<>
100<c< td=""></c<>
rs12203592
IRF4
C
T
T/T
CT(1x,2x)
T/T (3x)
C/C
1<t< td=""></t<>
0<t< td=""></t<>
11<t< td=""></t<>
</tbody>
Hirisplex SNPs
<tbody>
SNP
Gene
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
Europe
N29insA
MC1R
C
A
C/C
C(10x)
C/C(5x)
C/C
?
?
?
rs11547464
MC1R
G
A
G/G
G(7x
?
G/G
100<g< td=""></g<>
100<g< td=""></g<>
99<g< td=""></g<>
rs885479
MC1R
G
A
?
G(6x)
?
?
99<g< td=""></g<>
35<g< td=""></g<>
92<g< td=""></g<>
rs1805008
MC1R
C
T
C/C
C(6x)
C/C (2x)
C/C
99<c< td=""></c<>
100<c< td=""></c<>
93<c< td=""></c<>
rs1805005
MC1R
G
T
G/G
G(12x)
G/G (6x)
G/G
99<g< td=""></g<>
100<g< td=""></g<>
89<g< td=""></g<>
rs1805006
MC1R
C
A
C/C
C(11x)
C/C (6x)
C/C
100<c< td=""></c<>
100<c< td=""></c<>
99<c< td=""></c<>
rs1805007
MC1R
C
T
C/C
C(8x)
?
C/C
100<c< td=""></c<>
100<c< td=""></c<>
92<c< td=""></c<>
rs1805009
MC1R
G
C
G/G
G(5x)
G/G (4x)
G/G
100<g< td=""></g<>
100<g< td=""></g<>
99<g< td=""></g<>
Y152OCH
MC1R
C
A
C/C
C(7x)
?
C/C
?
?
?
rs2228479
MC1R
G
A
G/G
G(11x)
G/G (4x
G/G
100<g< td=""></g<>
76<g< td=""></g<>
93<g< td=""></g<>
rs1110400
MC1R
T
C
C/C
T(8x)
?
C/C
100<t< td=""></t<>
100<t< td=""></t<>
100<t< td=""></t<>
rs28777
SLC45A2
C
A
C/A
C(8x)
A/A (4x)
C/C
80<c< td=""></c<>
88<c< td=""></c<>
2<c< td=""></c<>
rs16891982
SLC45A2
C
G
C/C
CC(6x)
?
C/C
?
?
97 G
rs12821256
KITLG
T
C
T/T
T(8x)
T/T (3x)
T/T
100<t< td=""></t<>
100<t< td=""></t<>
86<t< td=""></t<>
rs12821256
KITLG
T
C
T/T
T(8x)
T/T (3x)
T/T
100<t< td=""></t<>
100<t< td=""></t<>
86<t< td=""></t<>
rs4959270
EXOC2
C
A
A/A
C(7x)
A/A (1x)
C/C
81<c< td=""></c<>
66<c< td=""></c<>
53<c< td=""></c<>
rs12203592
IRF4
C
T
T/T
CT(1x,2x)
T/T (3x)
C/C
1<t< td=""></t<>
0<t< td=""></t<>
11<t< td=""></t<>
rs1042602
TYR
C
A
C/C
C(6x)
C/C (3x)
C/A
99<c< td=""></c<>
100<c< td=""></c<>
63<c< td=""></c<>
rs1800407
OCA2
C
T
C/C
C(12x)
C/C()1x)
C/C
100<c< td=""></c<>
100<c< td=""></c<>
92<c< td=""></c<>
rs2402130
SLC45A2
G
A
G/A
GA(2x,4x)
A/A (1x)
G/G
41<a< td=""></a<>
93<a< td=""></a<>
77<a< td=""></a<>
rs12913832
OCA2-HERC2
A
G
G/G
G(3x)
G/G (1x)
A/A
4<g< td=""></g<>
0<g< td=""></g<>
71<g< td=""></g<>
rs2378249
ASIP/PIGU
A
G
A/A
A(6x)
A/A (1x)
A/A
86<a< td=""></a<>
85<a< td=""></a<>
88<a< td=""></a<>
rs12896399
SLC45A2
G
T
G/G
?
?
T/T
?
?
?
rs1393350
TYR
G
A
G/G
G(6x)
G/G (4x)
G/G
99<g< td=""></g<>
100<g< td=""></g<>
76<g< td=""></g<>
rs683
TYRP1
A
C
A/A
A(1x)
A/A (1x)
A/A
13<a< td=""></a<>
1<a< td=""></a<>
63<a< td=""></a<>
</tbody>
Lazaridis (http://www.biorxiv.org/content/biorxiv/suppl/2014/04/02/001552.DC2/001552-3.pdf),
Genotypes of the Loschbour, Stuttgart, and Motala12 individuals at the sites comprising three haplotypes associated with blue eyes in modern populations26. Coverage at each position is given in parentheses for the Motala12 sample.*These sites had genotype quality between 20 and 30 but passed other quality filters.
<tbody>
Haplotype
Blue-eye allele
SNP
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
BEH1
A
rs4778138
?
?
A/A
?
A/A (3x)
A/G
?
?
BEH1
C
rs4778241
A
C
C/C
C(7x)
C/C (5x)
A/C
40<c< td=""></c<>
23<c< td=""></c<>
BEH1
A
rs7495174
?
?
A/A
?
A/A (1x)
A/A
?
?
BEH2
T
rs1129038
?
?
T/T
?
T/T (3x)
C/C
?
?
BEH2
G
rs1291382
?
?
G/G
?
G/G (1x)
A/A
?
?
BEH3
C
rs916977
T
C
C/C
C(9x
C/C (2x)
C/C
10<c< td=""></c<>
26<c< td=""></c<>
BEH3
T
rs1667394
?
?
T/T
?
T/T (4x)
T/T
?
?
</tbody>
Lazaridis (http://www.biorxiv.org/content/biorxiv/suppl/2014/04/02/001552.DC2/001552-3.pdf),
Genotypes of the Loschbour, Stuttgart, and Motala12 individuals at the 13 sites comprising the haplotype found at high frequency in present blue-eyed individuals, along with haplotype asignment25. Coverage at each position is given in parentheses for the Motala12 sample.* These SNPs had genotype quality <30 but passed other quality filters; °the individual could not be genotyped at this locus.
<tbody>
SNP
Gene
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
Europe
rs4778241
OCA2-HERC2
A
C
C/C
C(7x)
C/C (5x)
A/C
40<c< td=""></c<>
23<c< td=""></c<>
78<c< td=""></c<>
rs1129038
OCA2-HERC2
C
T
T/T
T(5x)
T/T (3x)
C/C
4<t< td=""></t<>
0<c< td=""></c<>
71<c< td=""></c<>
rs12593929
OCA2-HERC2
G
A
A/A
A(7x)
A/A (2x)
A/A
37<a< td=""></a<>
58<a< td=""></a<>
97<a< td=""></a<>
rs12913832
OCA2-HERC2
A
G
G/G
G(3x)
G/G (1x)
A/A
4<g< td=""></g<>
0<g< td=""></g<>
71<g< td=""></g<>
rs7183877
OCA2-HERC2
C
A
C/C
C(1x)
?
C/C
92<c< td=""></c<>
70<c< td=""></c<>
90<c< td=""></c<>
rs3935591
OCA2-HERC2
T
C
C/C
C(9x)
T/C (7x)
C/C
21<c< td=""></c<>
27<c< td=""></c<>
82<c< td=""></c<>
rs7170852
OCA2-HERC2
T
A
A/A
A(9x)
A/A (7x)
A/A
20<a< td=""></a<>
27<a< td=""></a<>
81<a< td=""></a<>
rs2238289
OCA2-HERC2
A
G
A/A
A(3x)
A/A (3x)
A/A
32<a< td=""></a<>
29<a< td=""></a<>
84<a< td=""></a<>
rs3940272
OCA2-HERC2
T
G
G/G
G(1x)
?
?
21<g< td=""></g<>
27<g< td=""></g<>
81<g< td=""></g<>
rs8028689
OCA2-HERC2
C
T
T/T
T(3x)
T/T (2x)
T/T
59<g< td=""></g<>
61<g< td=""></g<>
93<g< td=""></g<>
rs2240203
OCA2-HERC2
C
T
T/T
T(3x)
T/T (5x)
T/T
36<t< td=""></t<>
61<t< td=""></t<>
93<t< td=""></t<>
rs11631797
OCA2-HERC2
A
G
G/G
G(4x)
?
G/G
18<g< td=""></g<>
26<g< td=""></g<>
80<g< td=""></g<>
rs916977
OCA2-HERC2
T
C
C/C
C(9x
C/C (2x)
C/C
10<c< td=""></c<>
26<c< td=""></c<>
81<c< td=""></c<>
haplotype
h1
h1
*
*
</tbody>
<tbody>
SNP
Gene
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
Europe
rs1800414
OCA2
T
C
?
T(3x)
?
?
100<t< td=""></t<>
41<t< td=""></t<>
100<t< td=""></t<>
rs1800407
OCA2
C
T
C/C
C(12x)
C/C()1x)
C/C
100<c< td=""></c<>
100<c< td=""></c<>
92<c< td=""></c<>
rs1545397
OCA2
A
T
A/A
A(1x)
?
A/A
97<a< td=""></a<>
8<a< td=""></a<>
92<a< td=""></a<>
rs4424881
APBA2
T
C
?
TC(1x,4x)
?
?
10<c< td=""></c<>
45<c< td=""></c<>
87<c< td=""></c<>
rs6119471
ASIP
G
C
C/C
C(3x)
C/C (3x)
C/C
36<c< td=""></c<>
100<c< td=""></c<>
100<c< td=""></c<>
rs2378249
ASIP/PIGU
A
G
A/A
A(6x)
A/A (1x)
A/A
86<a< td=""></a<>
85<a< td=""></a<>
88<a< td=""></a<>
rs4911442
ASIP
A
G
?
A(1x)
?
?
100<a< td=""></a<>
100<a< td=""></a<>
91<a< td=""></a<>
rs1042602
TYR
C
A
C/C
C(6x)
C/C (3x)
C/A
99<c< td=""></c<>
100<c< td=""></c<>
63<c< td=""></c<>
rs1126809
TYR
G
A
?
G(6x)
?
?
99<g< td=""></g<>
100<g< td=""></g<>
75<g< td=""></g<>
rs1393350
TYR
G
A
G/G
G(6x)
G/G (4x)
G/G
99<g< td=""></g<>
100<g< td=""></g<>
76<g< td=""></g<>
rs10831496
GRM5
G
A
?
G(2x)
?
?
80<g< td=""></g<>
76<g< td=""></g<>
31<g< td=""></g<>
rs683
TYRP1
A
C
A/A
A(1x)
A/A (1x)
A/A
13<a< td=""></a<>
1<a< td=""></a<>
63<a< td=""></a<>
rs2733831
TYRP1
A
G
?
G(3x)
?
?
6<g< td=""></g<>
1<g< td=""></g<>
60<g< td=""></g<>
rs1408799
TYRP1
T
C
?
C(1x)
?
?
22<c< td=""></c<>
1<c< td=""></c<>
66<c< td=""></c<>
rs1407995
DCT
T
C
?
C(1x)
?
?
82<c< td=""></c<>
24<c< td=""></c<>
82<c< td=""></c<>
rs12203592
IRF4
C
T
T/T
CT(1x,2x)
T/T (3x)
C/C
1<t< td=""></t<>
0<t< td=""></t<>
11<t< td=""></t<>
rs12821256
KITLG
T
C
T/T
T(8x)
T/T (3x)
T/T
100<t< td=""></t<>
100<t< td=""></t<>
86<t< td=""></t<>
rs642742
KITLG
T
C
?
?
?
?
?
?
?
rs28777
SLC45A2
C
A
C/A
C(8x)
A/A (4x)
C/C
80<c< td=""></c<>
88<c< td=""></c<>
2<c< td=""></c<>
rs35395
SLC45A2
T
C
?
T(1x
?
?
76<t< td=""></t<>
88<t< td=""></t<>
2<t< td=""></t<>
rs2402130
SLC45A2
G
A
G/A
GA(2x,4x)
A/A (1x)
G/G
41<a< td=""></a<>
93<a< td=""></a<>
77<a< td=""></a<>
rs12896399
SLC45A2
G
T
G/G
?
?
T/T
?
?
?
rs2470102
SLC45A2
G
A
G/G
G(8x)
A/A(5x)
A/A
92<g< td=""></g<>
75<g< td=""></g<>
1<g< td=""></g<>
rs4959270
EXOC2
C
A
A/A
C(7x)
A/A (1x)
C/C
81<c< td=""></c<>
66<c< td=""></c<>
53<c< td=""></c<>
rs1805009
MC1R
G
C
G/G
G(5x)
G/G (4x)
G/G
100<g< td=""></g<>
100<g< td=""></g<>
99<g< td=""></g<>
rs2228479
MC1R
G
A
G/G
G(11x)
G/G (4x
G/G
100<g< td=""></g<>
76<g< td=""></g<>
93<g< td=""></g<>
rs885479
MC1R
G
A
?
G(6x)
?
?
99<g< td=""></g<>
35<g< td=""></g<>
92<g< td=""></g<>
N29insA
MC1R
C
A
C/C
C(10x)
C/C(5x)
C/C
?
?
?
rs11547464
MC1R
G
A
G/G
G(7x
?
G/G
100<g< td=""></g<>
100<g< td=""></g<>
99<g< td=""></g<>
rs885479
MC1R
G
A
G/G
G(6x)
G/G (3x)
G/G
99<g< td=""></g<>
35<g< td=""></g<>
92<g< td=""></g<>
rs1805008
MC1R
C
T
C/C
C(6x)
C/C (2x)
C/C
99<c< td=""></c<>
100<c< td=""></c<>
93<c< td=""></c<>
rs1805005
MC1R
G
T
G/G
G(12x)
G/G (6x)
G/G
99<g< td=""></g<>
100<g< td=""></g<>
89<g< td=""></g<>
rs1805006
MC1R
C
A
C/C
C(11x)
C/C (6x)
C/C
100<c< td=""></c<>
100<c< td=""></c<>
99<c< td=""></c<>
rs1805007
MC1R
C
T
C/C
C(8x)
?
C/C
100<c< td=""></c<>
100<c< td=""></c<>
92<c< td=""></c<>
Y152OCH
MC1R
C
A
C/C
C(7x)
?
C/C
?
?
?
rs1110400
MC1R
T
C
C/C
T(8x)
?
C/C
100<t< td=""></t<>
100<t< td=""></t<>
100<t< td=""></t<>
rs12913832
OCA2-HERC2
A
G
G/G
G(3x)
G/G (1x)
A/A
4<g< td=""></g<>
0<g< td=""></g<>
71<g< td=""></g<>
rs3935591
OCA2-HERC2
T
C
C/C
C(9x)
T/C (7x)
C/C
21<c< td=""></c<>
27<c< td=""></c<>
82<c< td=""></c<>
rs2240203
OCA2-HERC2
C
T
T/T
T(3x)
T/T (5x)
T/T
36<t< td=""></t<>
61<t< td=""></t<>
93<t< td=""></t<>
rs4778241
OCA2-HERC2
A
C
C/C
C(7x)
C/C (5x)
A/C
40<c< td=""></c<>
23<c< td=""></c<>
78<c< td=""></c<>
rs1129038
OCA2-HERC2
C
T
T/T
T(5x)
T/T (3x)
C/C
4<t< td=""></t<>
0<c< td=""></c<>
71<c< td=""></c<>
rs12593929
OCA2-HERC2
G
A
A/A
A(7x)
A/A (2x)
A/A
37<a< td=""></a<>
58<a< td=""></a<>
97<a< td=""></a<>
rs7183877
OCA2-HERC2
C
A
C/C
C(1x)
?
C/C
92<c< td=""></c<>
70<c< td=""></c<>
90<c< td=""></c<>
rs7170852
OCA2-HERC2
T
A
A/A
A(9x)
A/A (7x)
A/A
20<a< td=""></a<>
27<a< td=""></a<>
81<a< td=""></a<>
rs2238289
OCA2-HERC2
A
G
A/A
A(3x)
A/A (3x)
A/A
32<a< td=""></a<>
29<a< td=""></a<>
84<a< td=""></a<>
rs3940272
OCA2-HERC2
T
G
G/G
G(1x)
?
?
21<g< td=""></g<>
27<g< td=""></g<>
81<g< td=""></g<>
rs8028689
OCA2-HERC2
C
T
T/T
T(3x)
T/T (2x)
T/T
59<g< td=""></g<>
61<g< td=""></g<>
93<g< td=""></g<>
rs11631797
OCA2-HERC2
A
G
G/G
G(4x)
?
G/G
18<g< td=""></g<>
26<g< td=""></g<>
80<g< td=""></g<>
rs916977
OCA2-HERC2
T
C
C/C
C(9x
C/C (2x)
C/C
10<c< td=""></c<>
26<c< td=""></c<>
81<c< td=""></c<>
</tbody>
8-Plex SNPs
<tbody>
SNP
Gene
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
Europe
rs1291382
HERC2
?
?
?
G/G
G/G (1x)
A/A
?
?
?
rs1545397
OCA2
A
T
A/A
A(1x)
?
A/A
97<a< td=""></a<>
8<a< td=""></a<>
92<a< td=""></a<>
rs16891982
SLC45A2
C
G
C/C
CC(6x)
?
C/C
?
?
97 G
rs885479
MC1R
G
A
?
G(6x)
?
?
99<g< td=""></g<>
35<g< td=""></g<>
92<g< td=""></g<>
rs1426654
SLC24A5
G
A
G/G
G/G(3x)
A/A (3x)
A/A
?
?
100 A
rs12896399
SLC45A2
G
T
G/G
?
?
T/T
?
?
?
rs6119471
ASIP
G
C
C/C
C(3x)
C/C (3x)
C/C
36<c< td=""></c<>
100<c< td=""></c<>
100<c< td=""></c<>
rs12203592
IRF4
C
T
T/T
CT(1x,2x)
T/T (3x)
C/C
1<t< td=""></t<>
0<t< td=""></t<>
11<t< td=""></t<>
</tbody>
Hirisplex SNPs
<tbody>
SNP
Gene
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
Europe
N29insA
MC1R
C
A
C/C
C(10x)
C/C(5x)
C/C
?
?
?
rs11547464
MC1R
G
A
G/G
G(7x
?
G/G
100<g< td=""></g<>
100<g< td=""></g<>
99<g< td=""></g<>
rs885479
MC1R
G
A
?
G(6x)
?
?
99<g< td=""></g<>
35<g< td=""></g<>
92<g< td=""></g<>
rs1805008
MC1R
C
T
C/C
C(6x)
C/C (2x)
C/C
99<c< td=""></c<>
100<c< td=""></c<>
93<c< td=""></c<>
rs1805005
MC1R
G
T
G/G
G(12x)
G/G (6x)
G/G
99<g< td=""></g<>
100<g< td=""></g<>
89<g< td=""></g<>
rs1805006
MC1R
C
A
C/C
C(11x)
C/C (6x)
C/C
100<c< td=""></c<>
100<c< td=""></c<>
99<c< td=""></c<>
rs1805007
MC1R
C
T
C/C
C(8x)
?
C/C
100<c< td=""></c<>
100<c< td=""></c<>
92<c< td=""></c<>
rs1805009
MC1R
G
C
G/G
G(5x)
G/G (4x)
G/G
100<g< td=""></g<>
100<g< td=""></g<>
99<g< td=""></g<>
Y152OCH
MC1R
C
A
C/C
C(7x)
?
C/C
?
?
?
rs2228479
MC1R
G
A
G/G
G(11x)
G/G (4x
G/G
100<g< td=""></g<>
76<g< td=""></g<>
93<g< td=""></g<>
rs1110400
MC1R
T
C
C/C
T(8x)
?
C/C
100<t< td=""></t<>
100<t< td=""></t<>
100<t< td=""></t<>
rs28777
SLC45A2
C
A
C/A
C(8x)
A/A (4x)
C/C
80<c< td=""></c<>
88<c< td=""></c<>
2<c< td=""></c<>
rs16891982
SLC45A2
C
G
C/C
CC(6x)
?
C/C
?
?
97 G
rs12821256
KITLG
T
C
T/T
T(8x)
T/T (3x)
T/T
100<t< td=""></t<>
100<t< td=""></t<>
86<t< td=""></t<>
rs12821256
KITLG
T
C
T/T
T(8x)
T/T (3x)
T/T
100<t< td=""></t<>
100<t< td=""></t<>
86<t< td=""></t<>
rs4959270
EXOC2
C
A
A/A
C(7x)
A/A (1x)
C/C
81<c< td=""></c<>
66<c< td=""></c<>
53<c< td=""></c<>
rs12203592
IRF4
C
T
T/T
CT(1x,2x)
T/T (3x)
C/C
1<t< td=""></t<>
0<t< td=""></t<>
11<t< td=""></t<>
rs1042602
TYR
C
A
C/C
C(6x)
C/C (3x)
C/A
99<c< td=""></c<>
100<c< td=""></c<>
63<c< td=""></c<>
rs1800407
OCA2
C
T
C/C
C(12x)
C/C()1x)
C/C
100<c< td=""></c<>
100<c< td=""></c<>
92<c< td=""></c<>
rs2402130
SLC45A2
G
A
G/A
GA(2x,4x)
A/A (1x)
G/G
41<a< td=""></a<>
93<a< td=""></a<>
77<a< td=""></a<>
rs12913832
OCA2-HERC2
A
G
G/G
G(3x)
G/G (1x)
A/A
4<g< td=""></g<>
0<g< td=""></g<>
71<g< td=""></g<>
rs2378249
ASIP/PIGU
A
G
A/A
A(6x)
A/A (1x)
A/A
86<a< td=""></a<>
85<a< td=""></a<>
88<a< td=""></a<>
rs12896399
SLC45A2
G
T
G/G
?
?
T/T
?
?
?
rs1393350
TYR
G
A
G/G
G(6x)
G/G (4x)
G/G
99<g< td=""></g<>
100<g< td=""></g<>
76<g< td=""></g<>
rs683
TYRP1
A
C
A/A
A(1x)
A/A (1x)
A/A
13<a< td=""></a<>
1<a< td=""></a<>
63<a< td=""></a<>
</tbody>
Lazaridis (http://www.biorxiv.org/content/biorxiv/suppl/2014/04/02/001552.DC2/001552-3.pdf),
Genotypes of the Loschbour, Stuttgart, and Motala12 individuals at the sites comprising three haplotypes associated with blue eyes in modern populations26. Coverage at each position is given in parentheses for the Motala12 sample.*These sites had genotype quality between 20 and 30 but passed other quality filters.
<tbody>
Haplotype
Blue-eye allele
SNP
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
BEH1
A
rs4778138
?
?
A/A
?
A/A (3x)
A/G
?
?
BEH1
C
rs4778241
A
C
C/C
C(7x)
C/C (5x)
A/C
40<c< td=""></c<>
23<c< td=""></c<>
BEH1
A
rs7495174
?
?
A/A
?
A/A (1x)
A/A
?
?
BEH2
T
rs1129038
?
?
T/T
?
T/T (3x)
C/C
?
?
BEH2
G
rs1291382
?
?
G/G
?
G/G (1x)
A/A
?
?
BEH3
C
rs916977
T
C
C/C
C(9x
C/C (2x)
C/C
10<c< td=""></c<>
26<c< td=""></c<>
BEH3
T
rs1667394
?
?
T/T
?
T/T (4x)
T/T
?
?
</tbody>
Lazaridis (http://www.biorxiv.org/content/biorxiv/suppl/2014/04/02/001552.DC2/001552-3.pdf),
Genotypes of the Loschbour, Stuttgart, and Motala12 individuals at the 13 sites comprising the haplotype found at high frequency in present blue-eyed individuals, along with haplotype asignment25. Coverage at each position is given in parentheses for the Motala12 sample.* These SNPs had genotype quality <30 but passed other quality filters; °the individual could not be genotyped at this locus.
<tbody>
SNP
Gene
Ancestral
Derived
Loschbour
La Brana-1
Motala12
Stuttgart
Africa
Asia
Europe
rs4778241
OCA2-HERC2
A
C
C/C
C(7x)
C/C (5x)
A/C
40<c< td=""></c<>
23<c< td=""></c<>
78<c< td=""></c<>
rs1129038
OCA2-HERC2
C
T
T/T
T(5x)
T/T (3x)
C/C
4<t< td=""></t<>
0<c< td=""></c<>
71<c< td=""></c<>
rs12593929
OCA2-HERC2
G
A
A/A
A(7x)
A/A (2x)
A/A
37<a< td=""></a<>
58<a< td=""></a<>
97<a< td=""></a<>
rs12913832
OCA2-HERC2
A
G
G/G
G(3x)
G/G (1x)
A/A
4<g< td=""></g<>
0<g< td=""></g<>
71<g< td=""></g<>
rs7183877
OCA2-HERC2
C
A
C/C
C(1x)
?
C/C
92<c< td=""></c<>
70<c< td=""></c<>
90<c< td=""></c<>
rs3935591
OCA2-HERC2
T
C
C/C
C(9x)
T/C (7x)
C/C
21<c< td=""></c<>
27<c< td=""></c<>
82<c< td=""></c<>
rs7170852
OCA2-HERC2
T
A
A/A
A(9x)
A/A (7x)
A/A
20<a< td=""></a<>
27<a< td=""></a<>
81<a< td=""></a<>
rs2238289
OCA2-HERC2
A
G
A/A
A(3x)
A/A (3x)
A/A
32<a< td=""></a<>
29<a< td=""></a<>
84<a< td=""></a<>
rs3940272
OCA2-HERC2
T
G
G/G
G(1x)
?
?
21<g< td=""></g<>
27<g< td=""></g<>
81<g< td=""></g<>
rs8028689
OCA2-HERC2
C
T
T/T
T(3x)
T/T (2x)
T/T
59<g< td=""></g<>
61<g< td=""></g<>
93<g< td=""></g<>
rs2240203
OCA2-HERC2
C
T
T/T
T(3x)
T/T (5x)
T/T
36<t< td=""></t<>
61<t< td=""></t<>
93<t< td=""></t<>
rs11631797
OCA2-HERC2
A
G
G/G
G(4x)
?
G/G
18<g< td=""></g<>
26<g< td=""></g<>
80<g< td=""></g<>
rs916977
OCA2-HERC2
T
C
C/C
C(9x
C/C (2x)
C/C
10<c< td=""></c<>
26<c< td=""></c<>
81<c< td=""></c<>
haplotype
h1
h1
*
*
</tbody>