Fig. 3: Common variant-based genome-wide and transcriptome-wide association analyses for East Asian samples. | Nature Communications

Fig. 3: Common variant-based genome-wide and transcriptome-wide association analyses for East Asian samples.

From: Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese

Fig. 3

The meta-analyzed genome-wide association results (generalized linear mixed-effect model) were displayed in a Manhattan plot and a QQ plot in (a and b), respectively. The Manhattan plot for the transcriptome-wide association study (linear regression model) projected the SNP-level signal to the gene level by assuming gene expression regulation as the mediator. Each tested gene-tissue/cell type pairs were marked as a dot or a hollow diamond if the significance passed the multiple testing adjustment. Genes with top-ranked associations were labeled, followed by the source from where the gene expression model was trained (c). The raw p-values are presented in (a–c). For each gene, we only labeled the one with the lowest p-value among tissue or cell types. The correlation between predicted and observed gene expression of TP63 in lung tissue samples was visualized in (d). Each dot denotes a lung tissue sample.

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