It came to light as a mournful vigil Friday for the nine black worshippers killed at Emanuel African Methodist Episcopal Church gave way to anger and protests in Charleston and the state capital Columbia.
The church, one of the most historic African-American places of worship, meanwhile reopened, three days after a bloodbath that fueled simmering racial tensions in the United States and reignited impassioned calls for gun-control laws.
A rambling 2,500-word manifesto on the website, laced with racist lingo and spelling errors, does not bear the 21-year-old suspected white supremacist's name.
Roof, who went on the run after Wednesday's shooting, was caught a day later in neighboring North Carolina and is in solitary confinement in jail charged with nine counts of murder.
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The FBI said it was "taking steps to verify the authenticity" of the website.
Somber mourning turned to anger Saturday, with a rally at the state legislature in Columbia, where the Confederate flag has been a focal point for controversy for years.
While some whites consider the Civil War-era flag an emblem of Southern regional pride and heritage, others -- black and white -- see it as a sinister symbol of white supremacy and racism.
Several hundred chanting demonstrators massed outside the state house, the Confederate flag flapping in the evening breeze.
Several politicians, including US President Barack Obama, weighed in on the controversy yesterday.
Former Republican White House hopeful Mitt Romney posted on Twitter: "it's time to take down flag in SC."
Obama, who said after the Charleston shooting the United States should closely examine its gun laws, also recalled firearms deaths statistics on Twitter yesterday.