Extended Data Fig. 4: Characterization of the csaQTL at 15q25.1.

(a) Boxplot of sample-level phenotype values for each individual, organized by genotype at the lead SNP. (N: C/C 297, C/T 194, T/T 32) (Bold line: Q2. Box: Q1-Q3. Whisker: furthest observation within 1.5xIQR of the box.) We also show the GeNA p-value. (b) UMAP of myeloid cells colored by neighborhood-level phenotype value (that is, correlation between cell abundance and dose of alternative allele per neighborhood). (c) Violin plot of neighborhood-level phenotype value distribution within CD14+ monocytes, CD16+ monocytes and dendritic cells. (d) Heatmap of expression across neighborhoods for genes with strong correlations in expression to the csaQTL neighborhood-level phenotype. Neighborhoods are arrayed along the x-axis by phenotype value. (e) UMAP of myeloid cells colored by cell type assignment to the CD16+ monocyte cluster. We also show the Pearson’s r value between neighborhood-level phenotype values and a binary encoding of CD16+ monocyte cluster membership per cell. (f) Boxplot of cluster-based CD16+ monocyte % myeloid cells trait value per OneK1K donor by genotype. (Box and whiskers defined as in subplot a). The csaQTL lead SNP explains 6.5% of variance in this phenotype. (g) Locus zoom plot with one marker per tested SNP, genomic position along the x-axis, and GeNA p-value on the y-axis. Each SNP marker is colored by LD value relative to the lead SNP. The lead SNP is labeled with a green diamond. The BCL2A1 eQTL lead SNP and primary sclerosing cholangitis risk lead SNP are labeled with purple triangles. (h) Diagram of genotypes for the csaQTL lead SNP and colocalizing associations to molecular, tissue and organism-level traits at this locus.