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. 2013 Mar 21;9(3):e1003372. doi: 10.1371/journal.pgen.1003372

Figure 6. Allele frequency and haplotype analysis for eye and skin color loci at 15q13.1.

Figure 6

(a,b) Allele frequency distributions for the SNPs most significantly associated with eye [HERC2 rs1291382; (a)] and skin [APBA2 rs4424881; (b)] in the HapmapIII [19] and HGDP [39] panels for the old world. Blue/orange shading corresponds to the frequency of the ancestral/derived alleles, as determined by comparison with the chimp reference sequence (assembly CGSC2.1/pan Tro2). Frequency values are presented in Table S3. c) Visual displays of the haplotypes extending from HERC2 to the second intron of APBA2 in Europeans from HapMap phase III (CEU) and HGDP (French, French Basque, North Italian, Tuscan, Sardinian, Orcadian, and Russian) panels. Haplotypes were inferred on the basis of 26 SNPs common to both datasets; blue and orange shades represent the ancestral and derived alleles, respectively. Haplotypes were ordered according to the ancestral/derived states at HERC2 rs1291382 and APBA2 rs4424881 (marked with red arrows), as follows: haplotypes bearing the ancestral alleles for both SNPs (Anc-Anc); haplotypes bearing the derived allele for HERC2 rs1291382 and the ancestral allele for APBA2 rs4424881 (Der-Anc); haplotypes bearing the ancestral allele for HERC2 rs1291382 and the derived allele for APBA2 rs4424881 (Anc-Der); and haplotypes bearing the derived allele for both SNPs (Der-Der).