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The grounding happened around the same time as reports about bomb threats against five flights, including a United flight. Federal officials said later the threats were not credible.
Shares of United Airlines were trading down about 2 percent around 9:40 a.m. when the news broke.
The total stoppage time was 39 minutes. The FAA originally cited automation issues as the cause for the halt. Shortly after, the agency announced that all United mainline flights were released from the groundstop.
United Airlines told CNBC that flight delays began around 9 a.m. ET "to ensure aircraft departed with proper dispatching information."
"Flights are now departing and we are accommodating our customers to their destinations," the company said.