Fig. 5

Cell type-specific effect of sc-caQTLs can be driven by trans-factors. a Box plot showing the chromatin accessibility of the OCR harboring rs12447029 in 20 individuals with different genotype of rs12447029 in MG. NFE2L2 motif position weight matrix aligned to reference and alternative allele at rs12447029. Violin plot showing the expression level of NFE2L2 across retinal cell types. Genome track of GRIN2A locus showing cell type-specific chromatin accessibility and positioning of rs12447029 within an OCR which is a predicted LCRE of GRIN2A. b Box plot showing the chromatin accessibility of the OCR harboring rs6859300 in 20 individuals with different genotype of rs6859300 in Rod, Cone, and BC. EPAS1 motif position weight matrix aligned to reference and alternative allele at rs6859300. Violin plot showing the expression level of EPAS1 across retinal cell types. Genome track of WWC1 locus showing cell type-specific chromatin accessibility and positioning of rs6859300 within an OCR which is a predicted LCRE of WWC1. c Violin plot showing distribution of gene expression levels of TFs in Rod and another cell type. These TFs have binding motifs perturbed by a sc-caQTL that has effect specifically in Rod but not in the other cell type. One-sided Wilcoxon rank sum test was performed to detect difference of gene expression levels of these TFs between Rod and the other cell type. The p-value and sample size n are indicated in the figure