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Table 2 Derived pigmentation gene variants under selection in different populations

From: Human pigmentation genes under environmental selection

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
  1. aSemiquantitative assessment of phenotypic effect, + weak , ++ medium, +++ strong.
  2. bNo single extended haplotype, competing selective pressures.
  3. cTagging SNPs in linkage disequilibrium with variants that may affect activity.
  4. dTransmission disequilibrium test (TDT) analysis performed on BTNS collection [86].
  5. eDiversity based test: Tajima D, Fu's Fs.
  6. fHaplotype length-based test: iHS, EHH, XP-EHH.
  7. gInferred from population size, geographical location.