By Harriet McLeod

CHARLESTON, S.C. (Reuters) - A white man was arrested on Thursday on suspicions he killed nine people at a historic African-American church in South Carolina after sitting with them for an hour of Bible study in an attack U.S. officials are investigating as a hate crime.

The mass shooting set off an intense 14-hour manhunt that ended when 21-year-old Dylann Roof was arrested in a traffic stop about 220 miles (350 km) north of Charleston, South Carolina, where the shooting occurred, officials said.

Wednesday's mass shooting at the almost 200-year-old Emanuel African Methodist Episcopal Church, comes after a year of turmoil and protests over race relations, policing and criminal justice in the United States. A series of police killings of unarmed black men has sparked a renewed civil rights movement under the "Black Lives Matter" banner.

Four pastors, including Democratic state Senator Clementa Pinckney, 41, were among the six women and three men shot dead at the church nicknamed "Mother Emanuel," which was burned to the ground in the late 1820s after a slave revolt led by one of its founders.

"The fact that this took place in a black church obviously raises questions about a dark part of our history," said U.S. President Barack Obama. "Once again, innocent people were killed in part because someone who wanted to inflict harm had no trouble getting their hands on a gun."

The United States has seen a series of mass shootings in recent years, including the 2012 massacre at Sandy Hook Elementary School, where a gunman killed 20 children and six adults. Democratic efforts to reform the nation's gun laws, protect by the Second Amendment of the U.S. Constitution, failed after that incident.

GIFT OF A GUN

A man who identified himself as Carson Cowles, Roof's uncle, told Reuters that Roof's father had recently given him a .45-caliber handgun as a birthday present and that Roof had seemed adrift.

"I don't have any words for it," Cowles, 56, said in a telephone interview. "Nobody in my family had seen anything like this coming."

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Roof was armed with a handgun but surrendered peacefully at his arrest, said Charleston Police Chief Greg Mullen.

In a Facebook profile apparently belonging to Roof, a portrait showed him wearing a jacket emblazoned with the flags of apartheid-era South Africa and of the former Rhodesia, now Zimbabwe, both formerly ruled by white minorities. Many of his Facebook friends were black.

Roof was arrested on two separate occasions at a shopping mall earlier this year for a drug offense and trespassing, according to court documents.

Roof's mother, Amy, declined to comment when reached by phone.

"We will be doing no interviews, ever," she said before hanging up.

Sylvia Johnson, a cousin of Pinckney, told MSNBC that a survivor told her the gunman reloaded five times during the attack despite pleas for him to stop.

"He just said, 'I have to do it. You rape our women and you're taking over our country," Johnson said.

U.S. Attorney General Loretta Lynch said her office was investigating whether to charge Roof with a hate crime motivated by racial or other prejudice.

Under federal and some state laws, such crimes typically carry harsher penalties, but South Carolina is one of just five U.S. states not to have a hate-crimes law.

RISING RACIAL TENSIONS

Demonstrations have rocked New York, Baltimore, Ferguson in Missouri and other U.S. 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 U.S. 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."

(Additional reporting by David Bailey in Minneapolis; Brian Snyder in Charleston; Julia Edwards in Washington; Emily Flitter and Alana Wise in New York; David Adams in Miami; Letitia Stein in Tampa, Florida; Randall Hill in Charleston, South Carolina; Alex Dobuzinskis in Los Angeles and Curtis Skinner in San Francisco; Writing by Scott Malone; Editing by James Dalgleish and Lisa Shumaker)