Runx1の標的遺伝子にSNPがあることで疾患につながることもある。例えば、リンパ球の自己寛容に関わる遺伝子のPDCD1(programmed cell death 1)の4番目のイントロンにあるRunx結合部位に変異(TGCGGTC→TGCAGTC)があると自己寛容に破綻を生じSLEを起こすことが知られている[13]。
^Robert B. Lorsbach, Jennifer Moore, Sonny O. Ang, Weili Sun, Noel Lenny, and James R. Downing (2003). “Role of RUNX1 in adult hematopoiesis: analysis of RUNX1-IRES-GFP knock-in mice reveals differential lineage expression”. Blood103 (7). doi:10.1182/blood-2003-07-2439. PMID14630789.
^B Lutterbach, S.W Hiebert (2000). “Role of the transcription factor AML-1 in acute leukemia and hematopoietic differentiation.”. Gene245 (2). doi:10.1016/S0378-1119(00)00014-7. PMID10717473.
^ abTahir H. Tahirov, Taiko Inoue-Bungo, Hisayuki Morii et al (2001). “Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta.”. Cell104 (5). doi:10.1016/S0092-8674(01)00271-9. PMID11257229.
^Jerónimo Bravo, Zhe Li, Nancy A. Speck & Alan J. Warren (2001). “The leukemia-associated AML1 (Runx1)--CBF beta complex functions as a DNA-induced molecular clamp.”. Nature Structure Biology8 (371). doi:10.1038/86264. PMID11276260.
^R. Katherine Hyde and P. Paul Liu (2010). “RUNX1 Repression Independent Mechanisms of Leukemogenesis by Fusion Genes CBFB-MYH11 and AML1-ETO (RUNX1-RUNX1T1)”. Journal of Cellular Biochemistry110 (5): 1039-1045. doi:10.1002/jcb.22596. PMID20589720.
^Ludmila Prokunina et al (2002). “A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans”. Nature Genetics32 (4): 666-669. doi:10.1038/ng1020. PMID12402038.