Fig. 2: Association results and functional prediction of lung cancer risk-associated potential splicing SNPs.
From: Deciphering associations between three RNA splicing-related genetic variants and lung cancer risk
a Manhattan plot of the overall results. There were 295 SNPs related to RNA splicing with a nominal P < 0.05, 14 of which remained with FDR < 0.20. The x-axis indicates the chromosome number and the y-axis shows the association P values with lung cancer risk (as −log10 P values). The horizontal blue line represents P values of 0.05, while the red line indicated the FDR threshold 0.20. Regional association plot, which shows the LD between the top SNP rs329118 on JADE2 (b), rs2285521 on GGA2 (c), and rs198459 on MYRF (d), and other SNPs in the region of 500 kb up- or downstream of the top SNP. Locations, functional prediction, and position weight matrix based Sequence Logo of three SNPs. JADE2 rs329118 (e) and GGA2 rs2285521 (f) are located within one CpG island and presented strong signals of active enhancer and promoter functions (indicated by H3K4 methylation, histone modification H3K27 acetylation, and DNase hypersensitivity, respectively). MYRF rs198459 (g) is located within one CpG island and presented strong signals of active enhancer and promoter functions (indicated by H3K4 methylation and DNase hypersensitivity, respectively). The panels were adapted from the UCSC Genome Browser. Three SNPs are located on the AP2B motif (e), the MYOD1 motif (f), and the ELK3 motif (g), respectively.
