An example of sQTL signal overlapping with GWAS signal near gene SP140. (a) The distribution of GLiMMPS P values around the sQTL exon (exon 7) in gene SP140. The black horizontal dashed line reflects the 10% FDR cutoff and red vertical lines mark the location of the sQTL exon. SNPs in linkage disequilibrium (r2 >0.8 in the CEU population) with the GWAS SNPs (blue asterisks) are shown in solid black dots, while other SNPs are shown in grey circles. The causal splicing SNP in exon 7 is shown in red triangle. Exon-intron structure is shown in the bottom with GWAS SNPs and the causal splicing SNP (rs28445040) marked at corresponding locations. (b) Boxplot showing the significant association of rs28445040 with exon inclusion level (ψ) of the SP140 exon 7 estimated by the CEU RNA-seq dataset. The size of each dot is scaled by the total number of splice junction reads for that individual. (c) The same boxplot using exon inclusion level (ψ) measured by quantitative RT-PCR.
Zhao et al. Genome Biology 2013 14:R74 doi:10.1186/gb-2013-14-7-r74