Extended Data Fig. 9: SMAD3 locus in asthma GWAS.
From: Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles
Rs17293632 in asthma GWAS (a) was prioritized and connected to SMAD3 gene by SCENT in myeloid cells (b). The panel a is a GWAS regional plot, with x-axis representing the position of each genetic variant and y-axis representing -log10(P) from GWAS (a two-sided P value). The rs17293632 has a significant caQTL effect, as shown in c and d. In panel c, the read coverage from single-cell ATAC-seq in each of donors with heterozygous genotype at this accessible region is presented, and at rs17293632, we observed allele-specific increased accessibility with C allele when compared T allele across donors. In panel d, normalized chromatin accessibility based on the read coverage for an individual after regressing out covariates is presented by the genotype of rs17293632 (CC, CT and TT). The horizontal bars within boxes indicate the median, and the lower and upper hinges represent 25% and 75% quantile. The upper whisker extends from the hinge to the largest value no further than 1.5 * inter-quartile range (IQR) from the hinge. The lower whisker extends from the hinge to the smallest value at most 1.5 * IQR of the hinge. All individual points are plotted as dots.
