According to the New York Post, the sample was taken by the Occupational Safety and Health Administration on Nov. 9. It was released last week to Assemblyman Micah Kellner.
Residents in the neighborhood have long complained about the air quality around the site.
The MTA told the Post that the levels of silica found underground in the preliminary findings "under no circumstance impacts air quality at street level."
Spokesman Kevin Ortiz said "silica does not float in the air, but rather drops to the ground."
The Second Avenue subway line will be 1.7 miles long. It's due to open in 2016.
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