The best replacement for cis is trans.

The best alternatives to cis are rated as following:
★★★★★  trans
★★★  cs
★★★  mis
★★  ccd
★  trans fatty acids
★  computer science
★  trans nmr
★  trans alkenes
★  ccd scanner
★  trans cyclohexane
  trans gender
  trans fats
  trans boiling point
  trans golgi
  paye
  ncaa hockey
  ehr
  cit
  ncaa
  ccd scanners
  bis
  cin
  trans proline
  ins
  trans chemistry
  digifant

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No companions for cis have been suggested so far.
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Google Trends

Scale is based on the average worldwide traffic of cis in all years. Click on graph for more.
cis
trans
cs