How does RNA relative abundance relate to SNPs and eQTLs?

Question

[rattus8]

I am looking at the GTex portal for significantly different expression of certain genes, within individual tissue types. Is this the same thing as saying that the gene has a significant normalized effect size associated with an eQTL in a tissue? (For instance: https://gtexportal.org/home/gene/PTEN#eQTLBlock)

I'm having trouble figuring out how the eQTL plays in, vs. SNP vs. plain old normalized transcript counts. I'm not sure why SNPs and variants come into play. Thank you!!

Answer 1

[GouthamAtla]

Differential gene expression is very different from an eQTLS gene (eGene) between tissues . They are completely different concepts. I would suggest to spend time in understanding an eQTL/eGene vs differential gene by reading literature.

PS: SNPs and variants (SNVs) are not very different.