Fig. 1

Schematic of eQTLs. a eQTLs are defined as sites in the genome where one of the alleles at a single nucleotide polymorphism (SNP) or copy number variation (CNV) is associated with greater average transcript abundance. Relative to disease risk, the allele that increases expression (here A) may be associated with protection (as here) or increased susceptibility (B). Note that there will always be some number of individuals with the susceptibility or risk genotype whose expression is well within the normal range or even tending in the opposite direction. This consideration suggests that gene expression may be a better indicator of risk than genotype alone, if it can be measured in the right tissue under the right conditions. b Cis-eQTLs are regulatory polymorphisms that influence transcription of a nearby gene on the same chromosome. Heterozygotes are expected to show allele-specific expression, since one of the alleles, in this case A, leads to increased transcription relative to the other (G). In general it is assumed that cis-eQTLs have differential affinities for transcription factors that bind to promoter, enhancer or repressor elements located within 250 kb on either side of the transcription start site. Trans-eQTLs, on the other hand, are polymorphisms at another locus, which increase or decrease expression at both alleles to a similar extent