Additional file 1 of Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations

Additional file 1: Table S1. Description of all phenotypes derived from each GWAS of East Asian and European individuals. Table S2. Comparison of the equivalent phenotypes derived from each GWAS of East Asian and European individuals. Table S3. Description of all phenotypes and statistics for baseline annotations derived from each GWAS of East Asian and European individuals. Table S4. Description of all phenotypes and statistics for evolutionary annotations derived from each GWAS of East Asian and European individuals with heritability z>7. Nominally significant enrichments (p < 0.05) are provided and FDR significant (q < 0.05) results are highlighted. Table S5. Traits from the UK Biobank included in the Phenome-Wide Association Study. The number of cases and controls and trait description are shown. Table S6. Significant association of Denisovan-introgressed variants with phenotypic traits from the Pan UKB in EAS. Beta value, SE, p-value, FDR q-value, gene annotation, predicted function, MAF, p value heterogeneity and q value heterogeneity are also reported. Table S7. Significant association of Neanderthal-introgressed variants with phenotypic traits from the Pan UKB in EAS. Beta value, SE, p-value, FDR q-value, gene annotation, predicted function, MAF, p value heterogeneity and q value heterogeneity are also reported. Table S8. Significant association of shared Denisovan- and Neanderthal-introgressed variants with phenotypic traits from the Pan UKB in EAS. Beta value, SE, p-value, FDR q-value, gene annotation, predicted function, MAF, p value heterogeneity and q value heterogeneity are also reported. Table S9. Significant association of Neanderthal-introgressed variants with phenotypic traits from the Pan UKB in EUR. Beta value, SE, p-value, FDR q-value, gene annotation, predicted function, MAF, p value heterogeneity and q value heterogeneity are also reported. Table S10. Significant association of Neanderthal-introgressed variants with phenotypic traits from the Pan UKB in CSA. Beta value, SE, p-value, FDR q-value, gene annotation, predicted function, MAF, p value heterogeneity and q value heterogeneity are also reported. Table S11. Significant association of Neanderthal-introgressed variants with phenotypic traits from the Pan UKB in MID. Beta value, SE, p-value, FDR q-value, gene annotation, predicted function, MAF, p value heterogeneity and q value heterogeneity are also reported. Table S12. Significant association of Denisovan-introgressed variants with phenotypic traits from the Pan UKB in CSA. Beta value, SE, p-value, FDR q-value, gene annotation, predicted function, MAF, p value heterogeneity and q value heterogeneity are also reported. Table S13. Significant association of shared Denisovan- and Neanderthal-introgressed variants with phenotypic traits from the Pan UKB in CSA. Beta value, SE, p-value, FDR q-value, gene annotation, predicted function, MAF, p value heterogeneity and q value heterogeneity are also reported. Table S14. Significant association of Neanderthal-introgressed variants with phenotypic traits from the Pan UKB in AMR. Beta value, SE, p-value, FDR q-value, gene annotation, predicted function, MAF, p value heterogeneity and q value heterogeneity are also reported. Table S15. Significant (FDR < 0.05) gene-set enrichments in the EUR PheWAS with Neanderthal-introgressed loci