Mourners embrace outside Emanuel African Methodist Episcopal Church after the street was re-opened a day after a mass shooting left nine dead during a bible study at the church in Charleston, South Carolina June 18, 2015. [Photo/Agencies]

Demonstrations have rocked New York, Baltimore, Ferguson in Missouri and other US cities following police killings of unarmed black men including Eric Garner, Freddie Gray and Michael Brown.

A white police officer was charged with murder after he shot Walter Scott, an unarmed black man, in the back in April in neighboring North Charleston.

The Southern Poverty Law Center, which researches US hate groups, said the attack illustrates the dangers that home-grown extremists pose.

"Since 9/11, our country has been fixated on the threat of Jihadi terrorism. But the horrific tragedy at the Emanuel AME reminds us that the threat of homegrown domestic terrorism is very real," the group said in a statement, referring to the Sept. 11, 2001 attacks on the United States.

There have been 4,120 reported hate crimes across the United States, including 56 murders, since 2003, the center said.

Other victims included three church pastors: DePayne Middleton Doctor, 49, Sharonda Coleman Singleton, 45 and Reverend Daniel Simmons, 74; Cynthia Hurd, a 54-year-old employee of the Charleston County Public Library, and Susie Jackson, 87; Ethel Lance, 70, Tywanza Sanders, 26, and Myra Thompson 59, an associate pastor at the church, according to the county coroner.

"This is going to put a lot of concern to every black church when guys have to worry about getting shot in the church," said Tamika Brown, who attended one of several overflow prayer vigils held at Charleston churches.

Police in Charleston responded to multiple bomb threats around the city through the course of the day on Thursday.

Three people survived the attack.

"It is a very, very sad day in South Carolina," Governor Nikki Haley, a Republican, in a tearful statement.

That grief rang hollow for some civil-rights activists, who noted that the state capital in Columbia still flies the Confederate flag, the rallying symbol of the pro-slavery South during the Civil War.

"The reality that racism is alive and well and that we have a problem with guns," said Clayborne Carson, founding director of the Martin Luther King Jr. Research and Education Institute at Stanford University. "People will throw up their hands and say 'how terrible' and the governor of South Carolina will put the Confederate flag of the state at half staff and then will get back to passing more laws that allow people to carry guns."