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Chicago Teachers Union members picket outside of the Chicago Public School headquarters on the fourth day of their strike in Chicago, Illinois, Sept. 13, 2012. REUTERS

Chicago's Board of Education filed a lawsuit Tuesday alleging the state of Illinois violated the civil rights of Chicago school children by maintaining two "separate" and "unequal" public education funding systems, one for Chicago and one for the rest of the state.

The lawsuit says Gov. Bruce Rauner and the state Board of Education discriminated against students in Chicago public schools. Citing the Illinois Civil Rights Act, the city is seeking to have the state's school funding system invalidated, the Chicago Tribune reported.

"The state treats CPS’ schoolchildren, who are predominantly African American and Hispanic, as second-class children, relegated to the back of the state’s education funding school bus," the lawsuit said. The suit noted that while Chicago public school students are 90 percent African-American and Hispanic, while the rest of the state's students are "predominantly white."

The Chicago Board of Education, which is led by Mayor Rahm Emanuel, filed the suit in Cook County Circuit Court on behalf of five African-American and Hispanic families with children attending Chicago Public Schools. The lawsuit notes that the Chicago public school system -- the country's third largest -- has 20 percent of the state's students but receives only 15 percent of the state's education funding.

The funding system "penalizes poor kids in poor school districts and rewards wealthy kids in wealthy school districts - just the opposite of what we should do,” Emanuel said, according to Reuters.

The lawsuit comes just two weeks after commission appointed by Rauner recommended the state abandon it's current funding system and adopt one that recognizes the added costs of educating children in poverty, USA Today reported.

Chicago's public school system is facing increasing pension payments. The city owes $733 million in pension payments this fiscal year, up from $676 million in 2016, Reuters reported. Last year, the city implemented a $250 million property tax increase to help fund a retirement plan for the city's teachers, USA Today said.