Does anyone know what percentage of single nucleotide polymorphisms within a gene body regulate expression of genes other than the one in which the SNP is found in? In a related question, what is the disadvantage of associating an intragenic GWAS SNP to the gene in which it is located? We'd be very grateful for any insights to these questions. Many thanks in advance.
I am curious too.
In my opinion, you can get an answer by analyzing eQTL data in GTEx (http://www.gtexportal.org/home/).
No, I don't think that would work. The significance threshold for trans-eQTLs is much higher than that for cis-eQTLs in most studies, (the p-value is around 10,000 times lower usually for trans-eQTLs) and certain loci, such as HLA, are heavily enriched for trans-eQTLs, which would bias the analysis.
Sorry, you might actually have to do an experiment to address the significance of SNPs. I don't think GWAS will ever have the resolution to answer this question directly.
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