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Table 4 Associations between SNP alleles with minor allele frequencies and eye colour categorised from photos of 107 Scots from Edinburgh.

From: Genetic determinants of hair and eye colours in the Scottish and Danish populations

Gene

Chr

SNP

positiona

Min A

MAFb

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

0.001d

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

  
  

rs11074304c

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

  1. a: Intron (Int), Exon or Untranslated region (UTR) position in the gene
  2. b: Minor allele frequency (MAF)
  3. c: alleles slightly out of Hardy Weinberg Equilibrium
  4. d: Significant using Bonferroni correction. Other p-values were corrected by empirical permutation
  5. e: Significant association in Duffy et al. 2006
  6. NA: No answer. Only observed among individuals with brown eye colour