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  <td align=left colspan=1><font face=Helvetica size=2>This slide is
  illustrates two categories of QTLs that modulate variability in transcript
  abundance.</font><br>
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  <td align=left colspan=1><font face=Helvetica size=2>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.</font><br>
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  <td align=left colspan=1><font face=Helvetica size=2>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.<span
  style="mso-spacerun: yes">&nbsp; </span>The way in which an upstream
  polymorphism influences a downstream difference in mRNA abundance can be very
  indirect. Effects can :</font><br>
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  <td align=left colspan=1><font face=Helvetica size=2><span
  style="mso-spacerun: yes">&nbsp;&nbsp; </span>a.<span style="mso-spacerun:
  yes">&nbsp; </span>cross tissue types (a polymorphic liver enzyme may affect
  CNS gene expression)</font><br>
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  <td align=left colspan=1><font face=Helvetica size=2><span
  style="mso-spacerun: yes">&nbsp;&nbsp; </span>b.<span style="mso-spacerun:
  yes">&nbsp; </span>cross time (the modulator is only expressed for one day
  during development but has permanent effects in adults),</font><br>
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  <td align=left colspan=1><font face=Helvetica size=2><span
  style="mso-spacerun: yes">&nbsp;&nbsp; </span>c.<span style="mso-spacerun:
  yes">&nbsp; </span>may be contingent on environmental factors (heat shock may
  trigger the expression of a polymorphic factor that affects mRNA abundance).</font><br>
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