File reporting the genomic location of all non-archaic variants used in this study.

(TXT)</p

Table reporting the GO enrichment results for the set of genes targeted by Denisovan, Neanderthal and non-archaic variants.

(XLSX)</p

Table reporting the primer and oligo sequences used in the <i>in-vitro</i> validation.

(XLSX)</p

aSNPs distribution across haplotypes.

Histogram showing the distribution of the Denisovan and Neanderthal allele frequency differences between archaic and non-archaic haplotypes. Negative values indicate putative archaic variants segregating at higher frequencies within non-archaic haplotypes. (PDF)</p

Biological processes putatively affected by SNPs within immune-related CREs.

For each ancestry the figure shows A) the overlap between the putative sets of target genes for each ancestry; B) the semantic similarity score estimates between the set of significantly enriched GO terms.</p

Table reporting the number of SNPs retained after each filtering step.

(XLSX)</p

Distribution of common-to-high-frequency aSNPs falling within CREs across 18 tissues.

Patterns of enrichment across the 18 different tissue types in Roadmap Epigenomics for the set of common-to-high-frequency aSNPs annotated within chromatin states associated with CREs, relatively to the matched background set of naSNPs. Histograms on top indicate the mean number of variants calculated across all cell types belonging to each tissue. Asterisks indicate BH-corrected Fisher’s exact test p-values: * = p ≤ 0.05, ** = p ≤ 0.01; *** = p ≤ 0.001; **** = p ≤ 0.0001 (for full statistical results see S7 Table).</p

Distribution of Neanderthal aSNPs identified within EUR across chromatin states and tissues.

Figure showing the patterns of enrichment across A) the 15 chromatin states for the entire set of Neanderthal aSNPs B) the 18 different tissues for the set of cis-regulatory Neanderthal variants segregating at common-to-high-frequencies in EUR. OR are computed relatively to the matched background set of naSNPs. Histograms on top indicate the mean number of variants annotated within each chromatin state (A) or within each tissue (B). The mean is respectively calculated across all 111 cell types and across the cell types belonging to each tissue. Asterisks indicate BH-corrected Fisher’s exact test p-values p ≤ 0.0001; *** = 0.0001 p ≤ 0.001; ** = 0.001 p ≤ 0.01; ** = 0.01 p ≤ 0.05. (PDF)</p

Overlap between target genes identified by Findley et al and this study.

(PDF)</p

Table reporting the enrichment results for the entire set of archaic variants annotated within each chromatin state.

(XLSX)</p