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Table 1 Pigmentation genes that are outliers based on the empirical distribution of different tests of positive selection

From: Exploring signatures of positive selection in pigmentation candidate genes in populations of East Asian ancestry

  Gene

    iHS

  LSBL

 Rsb-Eas-Afr

Rsb-Eas-Eur

  Tajima D

    H

   D*

   F*

Top 0.1%

        

EDAR

+(0.0019, 2)

++ (9.3E-06, 5)

++ (9.6E-04, 2)

+(0.0049, 1)

++(6.2E-04, 3)

   

CHB

MITF

    

++ (9.9E-04, 4)

+(0.0037, 3)

++ (2.1E-04, 5)

++ (1.8E-04, 6)

CHB/CHS/JPT

CHB/CHS/JPT

CHS/JPT

CHS/JPT

ATRN

    

+(0.0077, 2)

 

++ (9.6E-04, 3)

++ (9.4E-04, 6)

CHB

CHB

CHB/CHS

OCA2

 

++(5.6E-05, 5)

      

TRPM1

  

+(0.0012, 6)

+(0.0019, 5)

++(8.9E-04, 1)

   

CHS

TH

++(7.9E-04, 1)

 

+(0.0073, 1)

+(0.0028, 1)

    

KLHL7

      

++(8.81E-04, 5)

+(0.0010, 5)

CHB/CHS

CHB/CHS

TMEM33

    

++(1.72E-04, 9)

 

+(0.0029, 3)

+(0.0017, 3)

CHB/CHS/JPT

CHB

CHB

Top 1%

        

PMEL (SILV)

      

+(0.0051, 2)

+(0.0072, 2)

CHS

CHS

BNC2

    

+ (0.0026, 2)

+ (0.0056, 2)

+ (0.0051, 1)

+ (0.0039, 1)

CHB/CHS

CHS/JPT

CHS

CHS

EGFR

 

+ (0.0029, 3)

+ (0.0056, 1)

+ (0.0028, 1)

    

LYST

  

+ (0.0019, 1)

   

+ (0.0072, 1)

+ (0.0057, 1)

CHS

CHS

DCT

 

+ (0.0099, 1)

    

+(0.0064, 1)

+(0.0067, 1)

CHB

CHB

OPRM1

    

+ (0.0079, 1)

   

JPT

TYRP1

     

+(0.0081, 1)

  

CHS

MC1R

+(0.0073, 1)

 

+ (0.0027, 1)

     

MLPH

  

+(0.0015, 4)

  

+(0.0014, 3)

  

CHB/CHS/JPT

ADAM17

  

+(0.0015, 2)

+(0.0044, 2)

+(0.0021, 3)

   

JPT

CTSD

      

+(0.0045, 1)

+(0.0044, 1)

JPT

JPT

PDIA6

  

+(0.0069, 1)

  

+(0.0072, 1)

  

JPT

  1. The analysis was based on windows of 25 kilobases. In each cell, we indicate if the gene is in the top 0.1% (++) or 1% (+) of the empirical distribution for the relevant statistics. In parenthesis, we report the smallest p-value observed for any of the windows overlapping the gene, and the number of windows with p-values < 0.01. For the Site Frequency Spectrum tests (D, H, D*, and F*) we also indicate the East Asian populations in which we identified outlier 25 kb windows.