eQTL tries to regress each gene expression against each SNP, in order to find those regulatory elements. And eQTL uses "normal" samples, right? (by normal I mean "no disease" like those in 1000genome project)
GWAS compares SNPs between normal(control) and disease(test) samples, trying to find out those higher-frequency variants enriched for diseases.
Suppose now I've GWAS results at hands, say, top-ranking SNPs associated with schizophrenia, and I would like to find GWAS SNPs residing within eQTL.
So my questions are:
Can I use already available eQTL database, or should I establish such database myself? My concern is, each eQTL study from other groups has its own bias (sample size, population structure, ethnics...); so as far as I know, different eQTL database can vary dramatically, correct?
If to choose available eQTL database, what criterion should I take into accounts? For example, if the schizophrenia samples in GWAS are neuronal tissues, then should I refer to neuron-specific database? Or if it's blood, then blood-specific database? Also need to guarantee the ethnics consistent? Say both GWAS and eQTL database should be derived from Caucasians?