Definition of splicing eQTLs in RNA-Seq and arrays
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8.8 years ago
User 7754 ▴ 250

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 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 ( or sQTLseekeR (

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

Thank you!

genome RNA-Seq snp • 2.2k views

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