Denisovan-introgressed loci show 1.69-fold enrichment for coronary artery disease heritability in East Asians (p=0.003). No archaic introgression heritability enrichment in Europeans. East Asians carry 1.4% Neanderthal DNA versus 1.1% in Europeans. East Asians also carry Denisovan introgression absent in Europeans. No archaic introgression in Africans. Denisovan SNP rs62391664 lowers albumin/globulin ratio in East Asians (beta=-0.17, p=3.57e-7). Neanderthal alleles reduce bipolar/depression risk in East Asians (rs79043717 beta=-1.5, p=1.1e-7). Neanderthal alleles link to handedness in East Asians (rs145929965 beta=-3.54, p=6.45e-7). Shared Denisovan/Neanderthal alleles raise shortness of breath risk in East Asians (rs77589994 beta=5.27, p=1.1e-8). Shared alleles increase breast cancer risk in East Asians (rs12143332 beta=1.56, p=1.69e-7). Neanderthal alleles strongly associate with red hair in Europeans (rs60733936 beta=-0.86, p=4.49e-165). Neanderthal alleles alter alkaline phosphatase in Europeans (rs11244089 beta=0.1, p=3.69e-116). Neanderthal associations overrepresented for metabolic traits in Europeans (27.52-fold, p=6.61e-7). Neanderthal alleles link to medications like indapamide in Central/South Asians (rs732632 beta=-2.38, p=5.22e-7). No PheWAS associations survive correction in Admixed Americans. Genic and LoF-intolerant regions enrich heritability in both East Asians and Europeans. Background selection stronger in Europeans due to larger sample. Super-enhancers more enriched for non-albumin protein heritability in East Asians. Neanderthal loci in Europeans enrich for miRNA and transcription factor regulation.