As we enter the era of whole-genome sequencing, cataloging genetic variation between individuals in a species falls short in understanding the functional impact of this variation on an individual’s phenotype. There is variation of tolerance among different S. cerevisiae strains to the DNA damaging drug, 4-nitroquilione 1-oxide (4NQO). A clinical yeast isolate, YJM789, is very tolerant to 4NQO while S288c, a laboratory yeast strain, is sensitive. The genetic variation in 4NQO response is due Yrr1, a polymorphic transcription factor that shift the cellular response in resistance to 4NQO by changing rates of respiration which changes the metabolism of 4NQO. In ChIP-seq and RNA-seq we find that variation in transcription of genes required for response to 4NQO are poorly correlated with variation in Yrr1 binding upstream of these genes. SNQ2 encodes an ABC transporter which is strongly transcriptional induced in response to 4NQO with no change in Yrr1 binding. How the variation in transcription factors change RNA pol II transcription is under investigation. All the Yrr1 polymorphisms are outside the Zn-finger DNA binding domain and cluster at the C-terminus. By comparing the conservation of Yrr1 across yeast strain, a one residue in the C-terminus stood out as a potential phosphorylation site in Yrr1YJM789 and a second one changes the charge near a second phosphorylation site. Converting that site to a phosphomimic amino acid in the 4NQO-sensitive allele of Yrr1S96 confers 4NQO resistance similar to Yrr1YJM789. Yet how these single amino acid differences change the transcriptional outcome is unclear. We have used transcriptome, mutational analysis and protein-protein interactions to understand how these polymorphisms change the function of Yrr1.