genes map to eQTL/pQTL
You take a list of SNPs and a list of gene expression values and you plug it into something like this: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/


  So, how can it be possible that one gene (let say GENE22, location: 10-100) is mapped to eQTL(SNP within GENE22, location: 12) in one dietary condition but is not mapped to eQTL in another dietary condition if we are still speaking about the same gene and the same location of an eQTL? So, I am not quite sure what they mean or what they mapped there.


The SNP is associated with expression level changes in that gene for one dietary condition but that same SNP is not associated with expression level changes in another dietary condition. Its possible that the SNP never appears in samples from the other dietary condition.