Chicago Mayor Rahm Emanuel said Tuesday there remains an open question involving the sale of the James R. Thompson Center downtown: What’s going to happen to the CTA’s Clark and Lake Blue Line stop?

Illinois Gov. Bruce Rauner has wanted to sell the state office building for the past two years, as he said it would generate millions of dollars in property taxes for both the city and the state. But Emanuel told reporters Tuesday that he needs to know how the state plans to deal with the busy L station that sits underneath the Thompson Center.

If the station is torn down with the building, Emanuel estimates a replacement station could cost between $80 and $120 million dollars.

“I’m not gonna stick that on Chicago taxpayers,” Emanuel said. “The developer or the state has to do it.”

Rauner spokeswoman Eleni Demertzis said the state has always wanted to partner with the city in the redevelopment of the Thompson Center site, including the CTA station.

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The governor’s office has suggested the state could make up to $300 million off the deal, while the city could see as much as $45 million dollars in property taxes.

But the CTA station isn’t the only complication that’s bubbled up during talk of the sale. Downtown Ald. Brendan Reilly (42nd Ward) said another open question is the current zoning of the Thompson Center site.

Reilly said he thinks the governor’s office is banking on selling the property for much more than it’s currently worth. He said he zoning of the site only allows for a building of about a million square feet (about half the size of the Willis tower), but Reilly said the state wants to change that.

In Chicago, the power to change specific zoning rules rests in the hands of the aldermen. Reilly said he’s never increased the zoning of a site before, so it would be an “extraordinary circumstance” if he allowed a bigger building to replace Thompson Center.

“When I was elected, I promised my constituents that they should be able to rely upon the zoning that exists on the site today, that they don’t have to worry about middle-of-the-night zoning changes as a surprise from their aldermen,” Reilly said last month. “If you have an alderman who’s changing those classifications on a weekly, monthly, yearly basis, there’s no predictability in the neighborhood.”

But Reilly said as he has conversations with the mayor’s office about the Thompson Center sale, he’s been weighing some of the financial bonuses a bigger building could bring, like helping stabilize the state budget.

Lauren Chooljian covers city politics for WBEZ. Follow her @laurenchooljian.