The Syrian cell of the Sunni terror group has been fighting alongside rebel forces for most of the three-year civil war.
If JAN fighters deliver on their threats on Alawites in Syria, the attacks could trigger a wave of sectarian violence and escalate the ongoing civil war into a regional conflict.
Top Pentagon officials have recently cited the growing threat of sectarian violence in Syria as a main reason to avoid U.S. military action in the country.
"The conflict in Syria is intensifying and becoming more sectarian. The possibilities of state fragmentation are increasing, as are the risks of extremism and proliferation," Defense Secretary Chuck Hagel said during a speech in May.
"The old order in the Middle East is disappearing, and what will replace it remains unknown. There will continue to be instability in the region ... and we all must adjust accordingly," he said at the time.
Growing influence of Sunni terror groups like JAN and al Qaeda among rebel forces, along with Assad's strong support by Syria's Alawite population, could tear the country apart if sectarian tensions explode into all out war.
"I would not be surprised to see Syria break apart entirely," said Adm. James Stavridis, NATO Supreme Allied Commander, Europe and head of U.S. European Command, about the country’s post-Assad future in an interview with The Atlantic in May.
“When people say, ‘What does Syria look like the day after Assad?’ That's the wrong question. It's not what it will look like the day after; it's what will Syria look like a decade after,” Stavridis said.
But recent reports of chemical weapons attacks against rebel positions by Assad's troops has Washington preparing for military action in the country.
Administration officials said over the weekend they have “little doubt” that Assad's forces used poison gas to kill more than 1,300 people last week, and President Obama on Friday called the allegations “something that is going to require America's attention.”
U.S. warships, armed with long-range cruise missiles, are already on station off the coast of Syria ready to conduct surgical strikes against government positions in the country.
President Obama reportedly discussed Washington's military options in Syria with British Prime Minister David Cameron and French President François Hollande over the weekend.
Those talks came after an emergency meeting of Obama's national security team on Saturday at the White House.
The Obama administration is reportedly preparing legal justifications for a military strike against Syria without the United Nations' backing.
However, Hagel told reporters on Monday that Washington was only prepared to launch attacks in Syria with the blessing of the international community.