The end of special counsel Robert Mueller Robert (Bob) MuellerCNN's Toobin warns McCabe is in 'perilous condition' with emboldened Trump CNN anchor rips Trump over Stone while evoking Clinton-Lynch tarmac meeting The Hill's 12:30 Report: New Hampshire fallout MORE’s investigation is shifting the spotlight to federal prosecutors in President Trump Donald John TrumpOmar fires back at Trump over rally remarks: 'This is my country' Pelosi: Trump hurrying to fill SCOTUS seat so he can repeal ObamaCare Trump mocks Biden appearance, mask use ahead of first debate MORE's hometown.

While all eyes this weekend are on the Department of Justice and Mueller’s conclusions, the completion of the special counsel’s report won’t finish all the investigations into Trump.

The U.S. Attorney’s Office for the Southern District of New York (SDNY) is reportedly already carrying out a series of probes related to the president, including efforts focused on Trump's inaugural committee.

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It is also overseeing an investigation into potential campaign finance violations tied to the president.

Trump and his allies are well aware of the investigations and the dangers of the New York prosecutors.

The office is legendary for its ruthless and broad investigations and has shown a willingness to take on big names, from mafia bosses to celebrities and economic powerhouses.

Legal experts told The Hill that even as the Mueller probe ends, SDNY could pose an even greater threat to the president, his family and his businesses.

“That office has been very aggressive about going after high-profile targets,” said former federal prosecutor Kendall Coffey, who called the Manhattan attorney’s office “utterly fearless.”

“Anybody that might be in their bullseye ought to be mighty worried,” Coffey added.

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Jonathan Turley, a professor at George Washington University Law School, said charges pursued by SDNY could have a statute of limitations extending beyond Trump’s term, meaning Trump could be indicted once he leaves office.

“If the president was found to be part of a criminal conspiracy or violation, it’s possible that they could proceed with charges after the election,” said Turley, an opinion contributor to The Hill.

The White House and Trump attorney Jay Sekulow did not respond to requests for comment for this story.

Documents from the federal raids on former Trump attorney Michael Cohen Michael Dean CohenA huge deal for campaign disclosure: Trump's tax records for Biden's medical records Our Constitution is under attack by Attorney General William Barr Eric Trump says he will comply with New York AG's subpoena only after Election Day MORE released Tuesday indicated that federal prosecutors in New York are probing a potential campaign finance violation. Cohen has publicly implicated the president in the scheme to make payments to women alleging affairs with Trump, as have court filings from SDNY. Trump has denied any wrongdoing in the case.

The New York Times also reported Saturday that the Manhattan attorney’s office is conducting several investigations tied to the president, including one into his inaugural committee and two others linked to former Trump campaign chairman Paul Manafort Paul John ManafortOur Constitution is under attack by Attorney General William Barr Bannon trial date set in alleged border wall scam Conspicuous by their absence from the Republican Convention MORE.

A spokesperson for SDNY declined The Hill's request for comment.

A source close to Donald Trump Jr. Don John Trump'Tiger King' star Joe Exotic requests pardon from Trump: 'Be my hero please' Zaid Jilani discusses Trump's move to cancel racial sensitivity training at federal agencies Trump International Hotel in Vancouver closes permanently MORE dismissed any concerns over SDNY. Trump Jr. is overseeing the president's personal businesses alongside his brother Eric and has faced scrutiny over a 2016 Trump Tower meeting between Trump campaign officials and a Russian lawyer.

Legal sources told The Hill that as Mueller’s probe wound down, it’s possible he handed evidence not relevant to the Russia probe to other U.S. attorney's offices.

Mueller referred the Cohen investigation to SDNY after investigators on his team found evidence of crimes unrelated to Russian election interference, such as bank and wire fraud.

Coffey said that while Mueller had talented prosecutors on his team, his office lacked the longstanding structure and resources SDNY has in place. That could bolster any DOJ probes coming out of New York.

Several figures who were scrutinized as part of the Mueller probe have celebrated its conclusion, taking the lack of indictments issued as the investigation ended as a sign that they won’t be prosecuted as part of the Russia probe.

However, Mimi Rocah, a former assistant U.S. attorney for SDNY, said those figures could still face charges from other parts of the Justice Department.

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She said that because some figures such as Trump Jr. never interviewed with Mueller before the investigation concluded, those individuals could be targets of an investigation rather than just witnesses.

The experts also noted that many of the witnesses in the Mueller probe are now facing congressional inquiries. Democrats, who took over the House in January, have launched several investigations into Trump and his businesses.

The House Judiciary Committee alone has requested documents from 81 figures, including Trump Jr. and White House senior adviser Jared Kushner Jared Corey KushnerAbraham Accords: New hope for peace in Middle East Tenants in Kushner building file lawsuit alleging dangerous living conditions Trump hosts Israel, UAE, Bahrain for historic signing MORE, who is also Trump’s son-in-law.

“The congressional investigations remain a live torpedo in the water for any unindicted person,” Turley said.

Rocah said Mueller could hand over evidence that he uncovered in his probe to congressional investigations as long as it wasn’t part of a grand jury investigation and wasn't classified.

Jill Wine-Banks, who worked as an attorney on the Watergate investigation, said investigations launched by the state of New York could prove to be a bigger threat than those coming out of the U.S. attorney’s office.

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She said SDNY would have to follow the same Justice Department guidance Mueller did, which states a sitting president cannot be indicted. However, state prosecutors wouldn’t be held to the same standards.

The New York attorney general has personally targeted Trump before. The office last year sued the president over his foundation, demanding that it be dissolved and that he and his adult children be prevented from holding leadership roles at other charities, at least temporarily, over alleged “persistent illegality.”

And the Manhattan district attorney filed fraud charges against Manafort shortly after he was sentenced on federal charges. The maneuver was viewed by some as an attempt to stop Trump from potentially pardoning Manafort, as the president cannot pardon an individual for state charges.

“New York is his homebase and it’s where his corporation and foundation are,” Wine-Banks said of Trump, noting that the state and SDNY could also attempt to claim jurisdiction over the Trump inaugural committee and transition teams over their New York ties.