Table 1 Features of index SNPs in genome regions associated with pigmentation traits in the CANDELA sample

From: A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasia

    

Trait/Association (P value)

    

Skin

Hair

Eye

Region

SNP

Candidate gene

SNP annotation

MI

Categorical

Categorical

L (brightness)

C (saturation)

cos(H) (hue)

1q32

rs3795556

DSTYK

3’ UTR

2.1E-01

9.1E-01

6.8E-01

6.9E-03

4.0E-09

2.3E-01

5p13

rs16891982a,b

SLC45A2

F374L

1.3E-117

6.3E-66

1.3E-15

4.0E-17

5.4E-07

1.8E-04

6p25

rs12203592b

IRF4

Intronic

3.2E-10

2.0E-13

1.3E-12

3.2E-14

1.1E-03

4.5E-02

9p23

rs10809826a,b

TYRP1

Intergenic

1.1E-03

3.3E-02

1.0E-10

5.0E-16

2.0E-08

1.2E-02

10q26

rs11198112

EMX2

Intergenic

1.7E-10

6.1E-01

3.6E-01

4.9E-01

7.7E-01

4.9E-01

11q14

rs7118677a,c

GRM5

Intronic

1.1E-09

3.1E-06

6.1E-01

7.5E-01

4.8E-01

5.5E-01

11q14

rs1042602

TYR

S192Y

9.1E-10

2.3E-06

7.5E-01

3.9E-01

3.6E-02

7.8E-01

11q14

rs1126809a,c

TYR

R402Q

2.5E-09

6.2E-06

1.2E-04

5.3E-06

7.4E-02

7.7E-04

15q13

rs4778219c

OCA2

Intronic

8.3E-01

7.4E-01

4.7E-02

8.9E-02

6.2E-01

2.0E-01

15q13

rs1800407c

OCA2

R419Q

6.5E-09

5.5E-02

1.1E-02

7.2E-02

1.4E-07

4.8E-06

15q13

rs1800404b

OCA2

Synonymous/TFB

5.0E-11

7.0E-03

1.3E-11

5.0E-19

1.2E-06

4.1E-02

15q13

rs12913832b

HERC2

Intronic

1.0E-17

7.9E-105

1.0E-200

1.0E-200

5.7E-07

1.3E-92

15q13

rs4778249a,c

HERC2

Intronic

2.5E-06

1.2E-03

1.4E-10

2.5E-20

4.2E-15

5.1E-01

15q21

rs1426654b

SLC24A5

T111A

1.6E-130

1.0E-18

1.0E-26

7.9E-50

6.3E-45

4.4E-01

16q24

rs885479

MC1R

R163Q

1.9E-07

5.4E-02

5.6E-01

9.6E-01

8.0E-01

9.0E-01

19p13

rs2240751

MFSD12

Y182H

1.7E-10

8.2E-01

3.1E-01

9.6E-01

1.2E-01

9.1E-01

20q13

rs17422688

WFDC5

H97Y

5.2E-01

6.9E-01

8.2E-01

2.0E-01

9.0E-01

2.0E-08

22q12

rs5756492

MPST

Intronic

4.6E-03

9.9E-01

2.7E-02

9.5E-03

5.0E-08

1.5E-01

  1. Novel genomic regions are in bold. Genome-wide significant P values (<5 × 10−8) are in bold and underlined. Genome-wide suggestive significant P values (<10−5) are in bold
  2. MI: melanin index, L: lightness, C: chroma, H: hue
  3. aThese SNPs were obtained through imputation. Their imputation quality ‘info’ metric was ≥0.975, the median value being 0.993. The other SNPs were obtained from chip genotyping, and their ‘concordance’ metric was >0.9, the median value being 0.981
  4. bThese SNPs have been robustly associated with pigmentation traits in previous studies, and they explain a large proportion of the phenotypic variance in our sample (see Methods). These six SNPs were therefore used to condition the GWAS in subsequent analyses
  5. cThe independence of association signals of these SNPs from the main index SNPs in the same regions was confirmed by conditioned analyses
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