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. Author manuscript; available in PMC: 2018 Oct 9.
Published in final edited form as: Nat Genet. 2018 Apr 9;50(4):538–548. doi: 10.1038/s41588-018-0092-1

Figure 4. Chromatin and SCZ TWAS association at PPP2R3C.

Figure 4

Example association of PPP2R3C gene expression and SCZ and four nearby chromatin peaks. (A) locus schematic with all nearby genes and chromatin peaks; TWAS associated features highlighted in blue and green. (B–G left) Manhattan plots of marginal association statistics before and after conditioning on the TWAS predicted expression (colored/dark dots, respectively). Dashed line shows local significance threshold after Bonferroni correction for number of SNPs. (B–G right) Relationship between marginal GWAS/QTL association (y axis) and the correlation (x-axis) between TWAS predicted expression (GEpred estimated in the 1000 Genomes reference) and marginal GWAS/QTL association. The color of each point reflects the eQTL effect size of the expression used for GEpred and size of each point reflects absolute significance of the eQTL. (B) SCZ GWAS association; (C) PPP2R3C expression phenotype used for TWAS prediction and associated with SCZ/chromatin; (D) 1st TWAS associated H3k27ac peak in CEU; (E) 2nd TWAS associated H3k27ac peak in CEU; (F) 1st TWAS associated H3k4me1 peak in CEU; (G) 2nd TWAS associated H3k4me1 peak in CEU. See Supplementary Note, Supplementary Fig. 32, 33, 34 for additional examples and simulations.