A fire on a commuter train filled a rail car with smoke in the San Francisco Bay Area, injuring three people and snarling the Thursday morning rush hour.

Bay Area Rapid Transit trains are running again after systemwide delays. Four stations in the East Bay reopened after being closed for about five hours, but some delays remain.

BART is investigating what ignited the fire around 4:30 a.m. in the last car of a three-car train in east Oakland. Spokesman Jim Allison said 50 passengers were in the car and three were treated for injuries.

One person suffered smoke inhalation, another was treated for breathing difficulties and a third had an injured hand, the Oakland Fire Department said.

Crews are working to move the train and replace rails damaged in the incident, Allison said.

Earlier, the Lake Merritt, San Leandro, Fruitvale and Coliseum stations were closed, and service was suspended to Oakland International Airport.