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The National Weather Service issued the warning for southeastern Cook, northeastern Kankakee and central Will counties, which expired at 9:45 a.m.
The NWS said two to four inches of rain fell in the area, with up to another two inches of rain.
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ABC7 Meteorologist Tracy Butler said the storms are expected to move out of the area in the morning hours, with some potential for spotty showers through the afternoon.
A Ground Stop was issued at both O'Hare and Midway airports due to the thunderstorms.