Fig. 5

Putative regulatory variants are associated with differentially expressed genes and show cell-type-selective accessibility. A Examples of putative regulatory variants of A/J found in the enhancer region upstream of Ddhd1, Zfp619 and Rn4.5s. The putative regulatory variants are defined as variants disrupting TF footprints located in active enhancers (defined by H3K27ac). B Each DEG (5082, FDR < 0.05) is associated with an average of 0.4 putative regulatory variants, while non-DEGs are associated with only 0.14 variants. Random: 5000 genes are randomly selected from all expressed genes. C Putative regulatory variants have differential accessibility across cell types. More than half of the variants are accessible in more than 6 cell types, while 7% in only 1 cell type. D An example showing how putative regulatory variants with differential accessibility affect cell-type-specific gene expression. The variants locating near the TSS of Tekt5 are associated with TSS signal in neurons of C57BL/6J but not A/J, potentially resulting in upregulation of Tekt5 as shown in bulk RNA-seq. *FDR < 0.05