Chromatin-level QTLs in immune cells recover 4.5–22.6% more disease signals than expression QTLs alone
Across 3.47 million peripheral blood mononuclear cell nuclei from 922 donors, chromatin accessibility was treated as a heritable molecular trait, yielding 243,225 chromatin accessibility quantitative trait loci (caQTLs) across 28 immune cell types, 60% of them cell-type specific. Compared with single-cell expression QTLs (eQTLs), these loci colocalized with 4.5–22.6% more genome-wide association signals for 16 diseases and 44 blood traits; adding cell-type context, wider windows and multi-causal-variant models raised the share of inflammatory bowel disease loci with colocalization evidence from about 16% to about 65%.