Fig. 1: Identification of a potentially causative COVID-19 risk variant.
From: Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus
COVID-19 risk variants from GWAS were assessed for multiple mechanisms. All genome-wide-significant variants and linked variants are shown (GWAS) as are variants present in the Vindija Neanderthal12 risk haplotype. The circles indicate variants assessed for splicing changes (blue circles, SpliceAI18: ∆S score (0–1, where 1 is the most damaging)), and presence in cis-regulatory elements using open chromatin in 95 ENCODE overlaid DNase I datasets (red circles), normal human bronchial epithelial cells and scATAC-seq from fetal ciliated and alveolar epithelia34. Histone H3 modification tracks show the presence of marks associated with active transcription (H3K27ac) at enhancers (H3K4me1) and promoters (H3K4me3). Variants in open chromatin are given deepHaem damage scores (0–1) with sign indicating increased (−) or decreased (+) accessibility. The region shown is chr3:45,800,000–45,870,000, hg38. HSMM, human skeletal muscle myoblast; NHEK, normal human epidermal keratinocyte.
