Figure 1.

The Introgressed Region Encompassing the Genes TLR10, TLR1, and TLR6 on Chromosome 4

The genetic length of the region (chr4: 38,760,338–38,905,731; hg19) based on three recombination maps ranges from 0.04 cM to 0.1 cM (HapMap, 0.1 cM; deCode, 0.04 cM; and Hinch African American map, 0.08 cM).

(i) The gene structures for TLR10, TLR1, and TLR6 are displayed.

(ii) Predicted Neandertal haplotypes from the Neandertal ancestry map by Vernot et al.⁶ for Asians (green) and Europeans (blue).

(iii) Neandertal introgression posterior probabilities across polymorphic positions for Asians (blue solid lines) and Europeans (green solid lines) from the Neandertal ancestry map by Sankararaman et al.⁵ The chromosomal average introgression posterior probabilities are given as green and blue dashed lines.

(iv) Sharing of the Neandertal allele across archaic-like SNPs within seven core haplotypes: the Neandertal and Denisovan sequences and the seven modern human core haplotypes. The frequencies of Neandertal and Yoruba alleles for the archaic-like SNPs within each core haplotype are colored in red and black, respectively.

(v) Significantly associated SNPs with Helicobacter seroprevalence or allergic disease overlapping archaic-like SNPs are displayed.¹⁹, ²⁰