The storms moved through Madison, Wisconsin about 1 a.m., moving south at 50 mph, ABC7 Meteorologist Larry Mowry said. There were tornado warnings with the storm near Madison, he said.
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The Illinois Department of Transportation reported some trees down in Waukegan just before 4 a.m., as a result of the storms.
In north suburban Zion, the storms came with a lot of lightning, heavy rain and some high winds.
Near Zion Middle School, a few very large tree branches were blocking 27th Street. Some power lines appeared to be affected, too.
Some residents said they thought a tornado was coming through, so when part of a tree fell on their roof, they ran to the basement.
To their surprise, it wasn't a tornado -- instead, a quick moving wicked storm.
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In Chicago, siding from a two-story warehouse appeared to have been ripped off a Galewood building and tossed onto the Metra tracks, affecting the Metra Milwaukee District West.
WATCH | ABC7 AccuWeather 7-Day Forecast
Meg Reile, a Metra spokeswoman, said trains are not currently traveling past Bensenville on the line. In addition to the siding, there are wires across the tracks, she said.
WATCH: Chicago storm damage disrupts Metra service
Chicago storm damage disrupts Metra service
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There was not immediately an estimate of how soon service would resume.
And in Park Ridge, the winds were so strong, a huge part of the trunk splintered off an old oak tree, landing on top of a home, crushing the chimney and two cars in the driveway.
In Skokie, a large tree came down, blocking the ramp to the Edens at Old Orchard Road.
At the storm's height, ComEd said over 40,000 customers were without power.