"Looking historically at all the earthquakes that have happened in California, about 5 percent of the time earthquakes are followed by larger earthquakes", he said.
A spokesman for the California Governor's Office of Emergency Services said there were no reports of harm to the region.
He also said there were no reports of any damage or injuries. Near San Francisco International Airport, several jolts could be felt.
The quake knocked items off the 24-hour Safeway's shelves in San Leandro.
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East Bay residents are being warned to look out for aftershocks, which can happen days and weeks after a quake.
The quake hit the San Francisco area about 2.40am local time (11.40pm NZT) and lasted about 10 seconds, causing a "little bit of rolling motion and a sharp jolt", NBC Bay Area Chief Meteorologist Jeff Ranieri wrote on Twitter.
But there's also a chance that this was a foreshock, a precursor to a larger natural disaster.
In the past decade, there have been just four quakes about a four magnitude.
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'We live in quake country so we should do all the things they tell us to do, ' Knudsen said.
The USGS acknowledged though that the natural disaster was relatively deep for a Hayward Fault quake.
The Hayward Fault is capable of producing a 7-magnitude fault, which would have caused significantly more damage. "It may mean less likelihood of a larger quake to follow".
Knudson said the USGS had learned earthquakes, at least on the southern part of the Hayward Fault, occur every 140, 150 to 160 years. This fault zone runs from San Pablo Bay in the north to Fremont in the south-passing through Berkeley, Oakland, Hayward and Fremont.
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The last major quake along the Hayward fault happened in October of 1868, when a magnitude 6.8 hit the San Francisco Bay region, making it the most destructive natural disaster in the state's history.