Table 4

Associations between SNP alleles with minor allele frequencies and eye colour categorised from photos of 107 Scots from Edinburgh.

Gene

Chr

SNP

position^a

Min A

MAF^b

Ranked Eye colours

Shades

Brown vs blue

Brown vs other

p-values

p-values

OR

p-values

OR

p-values

OR

HPS3

3

rs7643410

int 1

G

0.08

0.04

2.9

rs2254913

int 5.1

A

0.37

0.006

0.03

1.7

0.003

2.6

0.01

1.9

rs2689229

int 5.2

A

0.46

0.01

0.02

1.8

0.004

2.5

rs2689230

int 5.3

G

0.23

0.04

0.046

2.2

0.02

2.6

0.04

2.1

rs2689234

int 6

G

0.49

0.03

0.009

2.3

rs6785780

int 8

T

0.41

0.03

0.02

2.3

rs2681092

int 15

T

0.38

0.02

0.01

2.3

0.04

0.5

KIT

4

rs17084733

3' UTR

A

0.11

0.02

4.3

0.04

3.6

DTNBP1

6

rs9476886

int 1

T

0.28

0.04

2.4

ERCC8

5

rs4647128

int 10

G

0.03

0.04

0.02

6.1

rs4235483

int 9

A

0.44

0.04

1.7

ERCC6

10

rs4253231

3'UTR

C

0.09

0.007

0.003

3.6

0.08

2.8

0.01

3.0

CYP2C8

10

rs11572177

int 8

G

0.30

0.04

1.9

DCT

13

rs9584233

int 6

T

0.11

0.03

3.4

0.03

2.4

OCA2

15

rs7495174

int 1.1

G

0.05

0.001^d

0.006

6.3

0.003

NA

0.009

5.9

rs7174027

int 1.2

A

0.06

0.009

3.1

0.003

NA

0.03

3.3

rs7179994

int 2.1

G

0.14

0.03

0.03

3.1

0.04

2.3

rs1597196

int 2.2

T

0.15

0.008

0.03

2.0

0.008

3.6

0.02

2.4

rs1470608

int 2.3

A

0.10

0.046

2.3

rs12324648

int 2.4

A

0.07

0.006

0.04

2.9

0.009

5.2

0.004

4.1

rs3794604

int 4

A

0.08

0.03

2.5

0.04

3.8

0.006

3.7

rs746861

int 6

C

0.45

0.02

1.8

rs7176632

int 16

T

0.18

0.0003

0.0008

2.9

0.0008

5.0

0.01

2.3

rs7173419

int 18.1

T

0.27

0.01

0.02

2.1

0.046

2.2

rs2594938

int 18.2

C

0.26

0.01

0.02

2.0

0.02

2.3

rs1562592

int 18.3

T

0.17

5.21 × 10^-5d

4.12 × 10^-5d

3.7

0.0009

4.2

0.0009

2.9

rs1448490

int 18.4

A

0.16

0.03

0.02

2.8

0.009

7.0

0.002

8.6

rs17674017

int 23.1

G

0.42

0.008

0.04

1.9

0.03

2.2

rs1498509

int 23.2

C

0.49

0.03

0.04

2.0

rs11631195

int 23.3

A

0.37

0.04

0.04

2.0

rs989869

int 23.4

C

0.38

0.02

rs1603784

int 23.5

A

0.23

0.01

0.03

2.6

rs11074304^c

int 23.6

A

0.42

0.04

0.04

2.2

GNAS

20

rs4810147

int 1

A

0.49

0.02

0.004

2.6

0.04

1.8

a: Intron (Int), Exon or Untranslated region (UTR) position in the gene

b: Minor allele frequency (MAF)

c: alleles slightly out of Hardy Weinberg Equilibrium

d: Significant using Bonferroni correction. Other p-values were corrected by empirical permutation

e: Significant association in Duffy et al. 2006

NA: No answer. Only observed among individuals with brown eye colour

Mengel-From et al. BMC Genetics 2009 10:88   doi:10.1186/1471-2156-10-88