I was wondering if there is a clear definition of what a splicing eQTL is. It seems to be defined differently when considering arrays compared to when considering RNA-Sequencing datasets.

In the context of exon arrays for example, sQTLs seem to be any SNP influencing the expression levels of a transcript (see http://www.nature.com/ng/journal/v47/n4/pdf/ng.3220.pdf). To find these variants we can perform linear associations using the expressions at each exon and the genotypes at each SNP. In the other hand, in the context of RNA-Seq, sQTL seems to refer only to SNPs influencing the relative expression of individual alternatively spliced isoforms, i.e. only SNPs associated with changes in the splicing ratios of a target gene, using methods such as GLIMMs (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333812/) or sQTLseekeR (http://www.nature.com/ncomms/2014/140820/ncomms5698/full/ncomms5698.html).

Can someone please clarify, is this is a semantic confusion in the field, or am I confused?

Thank you!