The association results between SNPs and PDCD4 transcript levels are corrected for multiple testing adjusted at a FDR threshold of 5%.
The genes with and without transcript accumulation polymorphism had similar percentage of SNPs, suggesting no or little correlation between transcript SNPs and transcript accumulation polymorphism.
We computed the linear relationships between SNPs and expression levels of exons, transcripts and genes, and the associations between gene CNVs and gene expression levels.
First, links between SNPs and Symatlas expression data for the relevant transcript in our current database version rely on Ensembl stable transcript IDs.
Similarly, standard interaction tests between SNPs and height, SNPs and smoking and SNPs and alcohol consumption were not significant.
In some instances, transcripts associated with SNPs in trans showed significant enrichment for certain gene ontology terms and pathways, suggesting linkages between SNPs and the activity of biological programs.
The results revealed several associations between gene copy numbers and the gene expression values, and also some associations between the SNPs and exon, transcript and gene expression values.
However, in the eQTL approach, associations between SNPs, transcript level, and phenotypes are analyzed individually.
When also transcript and exon results were studied in the gene level, we had together 721 associations between SNP and genes.
We then assessed the association between QTL-specific SNPs and each transcript annotated to the same locus.
