Extended Data Fig. 2: Association of Five Lead SNPs within the Chr3p21 Region. | Nature Genetics

Extended Data Fig. 2: Association of Five Lead SNPs within the Chr3p21 Region.

From: Expanded COVID-19 phenotype definitions reveal distinct patterns of genetic association and protective effects

Extended Data Fig. 2

(a) The y axis represents -log10(P-values) for the association between the three SNPs presented in the main text (stars) plus two additional SNPs more recently reported as lead SNPs for COVID-19 severity or susceptibility by HGI (circles; see Supplementary Note). The three colors of the SNP annotation shapes represent three independent signals (r2 < 0.04). The plotted points represent -log10(P-values) for the association with each phenotype in our analysis, where P-values are two-sided and based on an inverse-variance-weighted fixed-effects meta-analysis. The plotted points are colored by phenotype, and the point’s size corresponds to the MAF from the combined EUR, LAT, AA meta-analysis cohort. The black horizontal dotted line represents P = 0.05 and the red horizontal dotted line represents P = 5 × 10-8. Each SNP’s position and the genes within the chr3:45835417-45889921 (hg19) are shown below the main plot. For all five SNPs, we also show (b) pairwise r2 and (c) pairwise D’ calculated in the CEU population from 1000 Genomes Project.

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