L trains were running with delays due to a condition at Bedford Avenue station, the MTA said.
Debris on the tracks and switch problems caused delays and service changes Wednesday afternoon.
A smoke-filled station near Bryant Park snarled the 7 train, the MTA said.
1, 2, 3, 4, 5, 7, D, F, N, Q, R trains and Times Square shuttles were all disrupted, officials said.
The person was run over inside the 137th Street station in Hamilton Heights, the FDNY said.
LIRR trains were delayed 20 to 30 minutes and NJ Transit was delayed by up to an hour.
The MTA's Cold Weather Plan was in effect Tuesday morning, bringing service changes to several lines.
Service on the F, R, M and E lines were disrupted Tuesday evening.
The MTA was running fewer trains with local service, the MTA said.
After a fire thwarted early morning travelers on the commuter train, the LIRR is back on track.
1 trains resumed operation, with delays, after being suspended between South Ferry and Times Square.
NJ Transit commuters faced delays of up to 30 minutes Wednesday morning.
Crews were working to repair the rail at 59th Street, an MTA spokesman said.
An Amtrak power outage stalled their own trains and New Jersey Transit lines, officials said.
A broken rail caused major delays Thursday at about 5 p.m.
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