This slide is illustrates two categories of QTLs that modulate variability in transcript abundance.
	1. cis QTLs are defined as QTLs that are closely linked to the gene whose transcript is the measured trait. For example, a polymorphism in the promoter that affects the binding of a transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms in enhancers. They may also be polymorphisms in neigghboring genes.
	2. trans QTLs map far enough away from the location of the gene that gives rise to the transcript that is being measured so that we can be quite certain that the QTL is not IN the gene itself. The most blatant type of trans-QTL would be a polymorphism in a transcription factor. BUT in the majority of cases, the trans QTLs can be far removed in a mechanistic sense from the actual events modulating transcript abundance. That is why there are three overlappoing arrows above.  The way in which an upstream polymorphism influences a downstream difference in mRNA abundance can be very indirect. Effects can :
	a.  cross tissue types (a polymorphic liver enzyme may affect CNS gene expression)
	b.  cross time (the modulator is only expressed for one day during development but has permanent effects in adults),
	c.  may be contingent on environmental factors (heat shock may trigger the expression of a polymorphic factor that affects mRNA abundance).