Fig. 5: Cell-type-specific enrichment of GWAS traits varies depending on presence or absence of underlying genetic variation.

A (Upper) Bar chart depicting linkage disequilibrium score regression (LDSC) coefficients of ATAC peaks in any F2 sample compared to randomized genomic regions of equivalent size. A positive coefficient indicates an enrichment of GWAS loci in ATAC peaks. (lower) Bar chart depicting unadjusted − log10 p-values of LDSC regression coefficients for each GWAS trait. P-values are determined for regression coefficients through two-sided T tests. B (Upper) Bar chart depicting LDSC coefficients for regression comparing ATAC peaks that were differentially accessible between any line for F2 to ATAC peaks that were not differentially accessible. (Lower) Bar chart depicting unadjusted − log10 p-values of LDSC regression coefficients for each GWAS trait. P-values are determined for regression coefficients through two-sided T tests. C (Upper) Bar chart depicting LDSC coefficients of ATAC peaks that did not overlap a genetic variation compared to ATAC peaks that did overlap a genetic variation. A positive coefficient indicates an enrichment of GWAS loci in peaks without genetic variation (lower) Bar chart depicting unadjusted − log10 p-values of LDSC regression coefficients for each GWAS trait. P-values are determined for regression coefficients through two-sided T tests. D WashU Epigenome Browser Shot⁴⁷ of SNP rs4453556 in motor neurons. The SNP location is identified with the first red arrow and vertical black line. Matplot wrap is a lineplot showing expression (RNA-seq) of each of the samples, color-coded by a donor. Read counts from RNA-seq are displayed for each sample, as well as ATAC-seq. Source data are provided as a Source Data file.