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. Author manuscript; available in PMC: 2021 Jun 10.
Published in final edited form as: Nat Genet. 2021 Jun 3;53(6):861–868. doi: 10.1038/s41588-021-00875-2

Figure 4. Mapping and colocalisation of microglia eQTLs with various GWAS traits.

Figure 4

a. The numbers of eQTL genes discovered by two different methods, RASQUAL (left bar) or simple linear regression (right bar, LM) in three myeloid cell types at FDR 5% (see Online Methods). b. The number of shared eQTLs across three myeloid cell types obtained by the three-way Bayesian hierarchical model (Online Methods). The combination of genes that are eQTLs (closed dots) or non-eQTLs (open dots) across three different myeloid cell types are shown below each bar. A line connecting two dots indicates a shared eQTL between different cell types. c. Empirical prior probability of eQTL sharing among three different myeloid cell types obtained by the three-way Bayesian hierarchical model (Online Methods). The Y-axis shows the proportion of genes genome-wide and the dots connected by segment illustrate the shared genetic association. d. Colocalisation of microglia eQTLs with 146 GWAS traits. The x-axis shows the number of genes where PP3, the posterior probability of the microglia eQTL and GWAS association being driven by two independent causal variants, was greater than 0.5. The y-axis is the number of colocalised genes where the posterior probability of a single shared causal variant between a microglia eQTL and a GWAS locus (PP4) was greater than 0.5. We subdivided and colored GWAS traits as follows: purple: neurodegenerative diseases; red: blood cell trait; blue: traits related with intelligence; green: autoimmune diseases; yellow: neuropsychiatric diseases; gray: others. The line shows a log-normal linear regression fit with gray shaded area indicating the 95% prediction interval of the fit. e. Heatmap of PP4 for neuro-degenerative/psychiatric diseases, intelligence related traits and autoimmune diseases showing all genes and GWAS trait with a combined PP4 greater than 0.5. Gray cells indicate that the gene-trait combination was not tested because the GWAS locus was not significant (lead SNP P>10-6), or there were no GWAS summary statistics available for secondary hits (PTK2B and TREML3P).

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