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eQTL analysis -- SNP associations at different chromosomes

Hi All,

I have a quick question regarding the eQTL analysis. I am mainly looking for cis-eqtls. So I extracted all the SNPs at 500 kb upstream and downstream of the genes in my list, made new genotype data for these SNPs and then ran the analysis.

So Now after the association analysis and FDR correction, I can see that some SNPs across different chromosomes are associated to multiple genes. Should I expect to see these associations (trans-eqtls) based on the distance I selected for the SNP extraction?

Have I done anything wrong? Can anyone please guide me in this regard?

Thank you very much

rna-seq snps eqtl-analysis
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written by SHN • SHN

A naive question, might those be a cis-eQTL to one of your genes so you just select them by accident?

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written by Carambakaracho Carambakaracho

Thanks for your comment. good point! Does it explain why they are significant for the gene on the other chromosome?

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written by SHN • SHN

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