Fig. 5: Candidate causal genes nominated through both Hi–C and SMR approaches in twenty loci. | Nature Communications

Fig. 5: Candidate causal genes nominated through both Hi–C and SMR approaches in twenty loci.

From: Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes

Fig. 5: Candidate causal genes nominated through both Hi–C and SMR approaches in twenty loci.

The Manhattan plot depicts the IGAP GWAS signal with putative AD risk genes assigned to each locus through both Hi–C and SMR approaches. Red indicates that increased expression of the gene is predicted to increase risk for AD. Blue indicates that decreased expression of the gene is predicted to increase risk for AD. Gold indicates that the directionality of gene expression that is associated with increased disease susceptibility cannot be robustly inferred. These genes were prioritized if they either a) interact with an AD risk enhancer that contains an eQTL for this gene or b) were implicated in enhancer activity to gene expression association, but did not have significant expression to disease risk associations (SMR). ZYX and PTK2B showed opposite directions of expression associated with disease risk in monocytes and macrophages. Strongest associations are reported (macrophages in ZYX locus and monocytes in PTK2B locus). The TREM2 locus is not shown since a well replicated rare loss-of-function mutations were found in TREM23. The PICALM locus is not shown since the prioritized gene is not expressed in microglia.

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