Extended Data Fig. 3: Complete results for cell type-level disease associations for 74 diseases/traits and TMS FACS 120 cell types.

Each row represents a disease/trait and each column represents a cell type (number of cells in parentheses). Heatmap colors denote the proportion of significantly associated cells (FDR < 0.1 across all cells for a given disease). Squares denote significant cell-type–disease associations (FDR < 0.05 across all pairs of the 120 cell types and 74 diseases/traits; 597 significant pairs; MC test; Methods). Cross symbols denote significant heterogeneity in association with disease across individual cells within a given cell type (FDR < 0.05 across all pairs; 273 significant pairs; MC test; Methods). Heatmap colors and cross symbols are omitted for cell-type–disease pairs with nonsignificant cell-type–disease associations. Within the blood/immune block (40 cell types and 21 diseases/traits), 136 of 264 cell-type–disease pairs with significant association also had significant heterogeneity. Within the brain block (11 cell types and 21 diseases/traits), 64 of 133 cell-type–disease pairs with significant association also had significant heterogeneity. Within the other block (69 cell types and 32 diseases/traits), 54 of 146 cell-type–disease pairs with significant association also had significant heterogeneity. We discuss the results for FEV1/FVC. We identified 20 cell types associated with FEV1/FVC (FDR < 0.05), including 5 lung cell types and 15 cell types from other tissues. They can be categorized into 5 sets of associations: (1) type II pneumocyte (2) skin-related cells (3) smooth muscle cells (4) fibroblast-and-MSC-like cells (5) pericyte-like cells. The first 4 sets of associations are consistent with a previous work⁷⁵. The 5th set of pericyte associations is also plausible because pericytes are known to regulate lung morphogenesis⁷⁶. We note that the cell type associations from the lung are more likely to be causal and those from the other tissues are more likely tagging the causal cell types due to shared expression. Numerical results are reported in Supplementary Table 12.