The accident happened around 6:20 a.m. underneath the Route 25 overpass, according to Geneva police.
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Metra said train number 18 struck the teen. Rail traffic was shut down for more than two hours in Geneva, LaFox and Elburn.
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The incident remains under investigation by the Geneva Police Department, Metra and the Kane County Coroner's Office.
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Officials have not released the teen's name. An autopsy has been scheduled for Wednesday.
The Sun-Times Media Wire contributed to this report.