Two comments on the claim that the chr3 COVID risk factor is introgressed from Neanderthals: https://www.biorxiv.org/content/10.1101/2020.07.03.186296v1.full.pdf
1. The haplotype certainly looks Neanderthal, but the indel that is the lead variant is actually ~5% in AFR compared to 8% in EUR: https://useast.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=3:45834468-45835469;v=rs11385942;vdb=variation;vf=3801215 so if that's the causal variant then it pre-dates the haplotype. Easy to resolve with AFR GWAS.
2. I'm not sure where the 0.53cm/Mb recombination rate comes from. In the maps I have it's more like 0.14 which changes the P value from 0.0009 to 0.29. But I could be wrong. Can someone check? @spence_jeffrey_ In any case, that calculation seems sensitive to the rate.
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