Fig. 4: FOXP4 expression in the lung.
a, The lead variant rs9367106 was not found in the GTEx dataset, but a proxy variant (rs12660421, chr6: 41,520,640) in high LD (r2 = 0.97, rs12660421-A allele is correlated with the long COVID risk allele rs9367106-C) showed a significant eQTL after multiple testing correction, increasing FOXP4 expression in the lung (P = 5.3 × 10−9, NES; expression with GA genotype compared to expression with GG, normalized to 0) = 0.56; GTEx V8 lung samples with GG genotype, n = 483, GA genotype, n = 32; https://gtexportal.org/home/snp/rs12660421). For other tissues, see multitissue eQTL plot in Supplementary Fig. 6. b, Colocalization analysis using eQTL data from GTEx v8 tissue type and long COVID GWAS meta-analysis association data (Supplementary Note). Plots illustrate −log10 P value for long COVID (x axis) and for FOXP4 expression in the lung (y axis), regional association of the FOXP4 locus variants with long COVID (top right) and regional association of the FOXP4 variants with RNA expression measured in the lung in GTEx (bottom right). Variants are colored by 1000 Genomes European-ancestry LD r2 with the lead variant (rs12660421) for FOXP4 expression in lung tissue (the most significant long COVID variant overlapping the GTEx v8 dataset (rs9381074) also annotated). c, Human Protein Atlas RNA single-cell type tissue cluster data (transcript expression levels summarized per gene and cluster) of lung (GSE130148) showing FOXP4 expression in unaffected individuals. The values were visualized using log10 (pTPM + 1) values. Each annotation is taken from the clustering results performed in the Human Protein Atlas. pTPM, protein transcripts per million.
