1, 2, 3, 4, 5, 7, D, F, N, Q, R trains and Times Square shuttles were all disrupted, officials said.
There were also delays on J and M lines and on southbound 4 and 6 trains on Tuesday morning.
Signal problems disrupted the 1, 2 and 3 subway lines in most of Manhattan, the MTA said.
Passengers had to get on a later train headed to the city, an Amtrak spokesman said.
The MTA said to expect systemwide delays of up to 20 minutes on the LIRR during the evening commute.
Penn Station closed down after signal problems stopped LIRR, Amtrak and NJ Transit trains.
Signal problems at New York Penn Station snarled trains to and from Manhattan.
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