Fig. 4: GWAS and eQTLs locus zoom plot for gene DEDD uniquely colocalized with axis-QTLs. | Nature Communications

Fig. 4: GWAS and eQTLs locus zoom plot for gene DEDD uniquely colocalized with axis-QTLs.

From: Integrating axis quantitative trait loci looks beyond cell types and offers insights into brain-related traits

Fig. 4: GWAS and eQTLs locus zoom plot for gene DEDD uniquely colocalized with axis-QTLs.

We present locus zoom plots (negative log10-based two-sided p-value) of a 1-Mb region surrounding the DEDD gene (chromosome 1:160,722,754–161,717,430 in hg38 genomic positions) across multiple datasets: AD GWAS, meta-sc-eQTLs (from seven cell types), MetaBrain bk-eQTLs, and BASIC axis-QTLs from PC0 to PC6. The darkness of the point reflects its linkage disequilibrium (LD) coefficient (R2) with the sentinel variant in the locus. The posterior probability of colocalization (PP4 in coloc) is indicated in each panel. Interestingly, this locus cannot be colocalized with any sc-eQTLs, shows moderate evidence of colocalization with bk-eQTLs, but can be colocalized with axis-QTLs from PC0 and PC1. As shown in Supplementary Fig. 16, the sc-eQTLs effects for many variants tend to have opposite effects across cell types and can cancel each other in bk-eQTLs analysis. This example demonstrates the importance of separating shared and distinct regulatory effects across cell types using axis-QTLs.

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