Table 2

Derived pigmentation gene variants under selection in different populations

Gene

SNP

Change/position

Skin

Eye

Hair

Selectiona


European

MC1R

Multiple

Coding , nonsynonymous

++

-

+++

+++b,e

ASIPc

rs4911442*T/C

(C) 3' distal/NCOA6 intron

+

-

+

++f

OCA2

rs12913832*T/C

(C) 5' distal/HERC2 intron86

+

+++

+

+++e,f

TYR

rs1042602*C/A

(A) Ser192Tyr (TCT to TAT)

+

+

+

++

TYR

rs1126809*G/A

(A) Arg402Gln (CGA to CAA)

+

+

+

++

TYRP1c

rs1408799*T/C

(C) 5' distal

+

+

+

+f

DCTc

rs1407995*C/T

(T) Intron 6

-

+

-

+d

SLC24A5

rs1426654*G/A

(A) Ala111Thr (GCA to ACA)

+++

+

+

+++f

SLC45A2

rs16891982*G/C

(C) Leu374Phe (TTG to TTC)

+++

+

+

+++f

IRF4

rs12203592*C/T

(T) Intron 4

++

++

++

+b

KITLGc

rs12821256*T/C

(C) 5' distal

++

-

++

+e,f

Asian

MC1R

rs885479*G/A

(A) Arg163Gln (CGA to CAA)

+

-

+

++b

OCA2

rs1800414*A/G

(G) His615Arg (CAT to CGT)

++

-

+

+++

OCA2

rs74653330*G/A

(A) Ala481Thr (GCC to ACC)

++

-

+

+++

DCTc

rs1407995*C/T

(T) Intron 6

+

-

+

+

KITLGc

rs12821256*T/C

(C) 5' distal

++

-

+

+

Oceania

OCA2

Gly775Asp

(A) (GGT to GAT)

+++

+++

+++

Driftg

TYRP1

Arg93Cys

(T) (CGC to TGC)

+

+

+++

Driftg

African

SLC24A5

rs1426654*G/A

(G) Ala111Thr (GCA to ACA)

+++

+++

+++

+++f

SLC45A2

rs16891982*G/C

(G) Leu374Phe (TTG to TTC)

+++

+++

+++

+++f

KITLGc

rs642742*T/C

(T) 5' distal

+++

+

+

+++f


aSemiquantitative assessment of phenotypic effect, + weak , ++ medium, +++ strong.

bNo single extended haplotype, competing selective pressures.

cTagging SNPs in linkage disequilibrium with variants that may affect activity.

dTransmission disequilibrium test (TDT) analysis performed on BTNS collection [86].

eDiversity based test: Tajima D, Fu's Fs.

fHaplotype length-based test: iHS, EHH, XP-EHH.

gInferred from population size, geographical location.

Sturm and Duffy Genome Biology 2012 13:248   doi:10.1186/gb-2012-13-9-248