Fig. 4: AD GWAS-QTL colocalization results.

a Number of AD GWAS loci with identified QTL colocalizations (PP4 > 0.75), stratified by QTL molecular phenotype and GWAS ancestry and novelty endpoints, colored in red—if previously reported—or blue—if novel. Bold or pale color hue represents loci identified in the multi-ancestry or European ancestry AD GWAS, respectively. PP4 corresponds to the posterior probability of whether a shared causal variant exists in the region (Methods). b Number of genes with identified QTL colocalizations (PP4 > 0.75), stratified by QTL molecular phenotype type. The inset heatmap represents the number of QTL endpoints per QTL type (x-axis) for each of the four genes supported by all QTL types (y-axis); barplot shows aggregated cross-QTL support per gene. c Genotype-phenotype association p-values of the CRAT locus. Panels illustrate CRAT pQTL signal in ARIC EA plasma (top) and GWAS signal for AD (middle) and GWAS signal for increased levels of 2-methylmalonylcarnitine (bottom). d Genotype-phenotype association p-values of the CD207 locus. Panels illustrate CD207 eQTL signal in GTEx skin not exposed to sun (top), ImmuNexUT myeloid dendritic cells (mDC) (middle) and GWAS signal for AD (bottom). Lead GWAS variant mapped to AD risk allele is typed and illustrated by a triangle-shaped point pointing upwards, indicating allele association with positive phenotype effect. Linkage disequilibrium between loci is quantified by squared Pearson coefficient of correlation (r2). P-values correspond to nominal GWAS and QTL associations, derived from multiple regression two-sided t-tests.