Fig. 4: Impact of disease on colocalizations. | Nature Genetics

Fig. 4: Impact of disease on colocalizations.

From: Cell state-dependent allelic effects and contextual Mendelian randomization analysis for human brain phenotypes

Fig. 4

a, Overview of colocalizations (PP.H4 > 0.8) aggregated across cell types for 30 CNS traits, indicating the total number of colocalizations for a given trait and the proportion with a disease interaction. b, Colocalization between TP53INP1 expression in oligodendrocytes and AD in the full cohort (left, PP.H4 = 0.91) and the control-only cohort (right, PP.H4 = 0.04). Each point represents the −log10(P) for an SNP and its association with the gene (top) and disease (bottom). c, Cis-eQTL plot showing the effect of disease samples in the full cohort (n = 391) on the association between the lead colocalized SNP rs4582532 and TP53INP1 expression in oligodendrocytes. The P values for ‘all’ represent the t statistic for the M1 models, whereas the P values for AD, PD and MS represent the P value from the interaction with genotype within the M2 model. The ‘control’ P value represents the effect of genotype on expression after accounting for interaction effects. d, Colocalization between RAB38 expression in excitatory neurons and behavioral frontotemporal dementia in the full cohort (left, PP.H4 = 0.81) and the control-only cohort (right, PP.H4 = 0.06). e, Cis-eQTL plot showing the effect of disease samples in the full cohort (n = 391) on the association between the colocalized lead SNP rs16913634 and RAB38 expression in excitatory neurons. Elements of the boxes show the center line (median), box limits represent upper and lower quartiles and whiskers represent upper and lower quartiles ±1.5× IQR. All data points have been included. f, Colocalization between PEX13 expression in excitatory neurons and MS in the full cohort (left, PP.H4 = 0.08) and the control-only cohort (right, PP.H4 = 0.87). g, Cis-eQTL plot showing the effect of disease samples in the full cohort (n = 391) on the association between the colocalized lead SNP rs11772842 and PEX13 expression in excitatory neurons. h, Comparison of colocalizations discovered in the full mixed disease-case and control dataset (n = 391) versus control samples only (n = 183).

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