Extended Data Fig. 7: LZTFL1 is a direct target of rs17713054.
From: Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus
a, NuTi Capture-C and Micro Capture-C from the rs17713054 enhancer in Endothelial cells (HUVEC) shows specific interaction with only the promoter of LZTFL1 and an upstream CTCF site. CTCF track shows binding of the CCCTC-binding factor which acts as a boundary. b, ENCODE ChIP-seq for the active chromatin mark (H3K27ac), the repressive chromatin mark (H3K27me3) and EZH2, a member of the Polycomb Repressive Complex 2, in endothelial (HUVEC) and normal human lung fibroblast (NHLF) cells. Green bar denotes the 3C regulatory domain as identified by 3 C analysis. c, ENCODE DNase I seq tracks from a range of cell types and tissues, including airway epithelium and bronchial epithelium, where the rs17713054 enhancer is active. In these cell types the LZTFL1 promoter is DNase I accessible, but neither the CCR9 promoter nor the SLC6A20 promoter are. Region shown is chr3: 45,730,000-45,930,000 (hg38). d, Paired accessibility analysis of read counts per kilobase (RPK) over the LZTFL1 and SLC6A20 promoters and the rs17713054 enhancer in 156 ENCODE, immune and erythroid open chromatin datasets. Only the LZTFL1 promoter is widely accessible in the same cells as the affected enhancer.
