P1 and P are glycosphingolipid antigens synthesized by the -encoded α1,4-galactosyltransferase, using paragloboside and lactosylceramide as acceptor substrates, respectively. In addition to the compatibility aspects of these histo-blood group molecules, both constitute receptors for multiple microbes and toxins. Presence or absence of P1 antigen on erythrocytes determines the common P (P1P) and P (P1P) phenotypes. transcript levels are higher in P individuals and single-nucleotide polymorphisms (SNPs) in noncoding regions of , particularly rs5751348, correlate with P/P status. Despite these recent findings, the molecular mechanism underlying these phenotypes remains elusive. The In(Lu) phenotype is caused by Krüppel-like factor 1 () haploinsufficiency and shows decreased P1 levels on erythrocytes. We therefore hypothesized KLF1 regulates expression. Intriguingly, -specific sequences including rs5751348 revealed potential binding sites for several hematopoietic transcription factors, including KLF1. However, KLF1 binding did not explain -specific shifts in electrophoretic mobility-shift assays and small interfering RNA silencing of did not affect transcript levels. Instead, protein pull-down experiments using but not oligonucleotide probes identified runt-related transcription factor 1 (RUNX1) by mass spectrometry. Furthermore, RUNX1 binds alleles selectively, and knockdown of significantly decreased transcription. These data indicate that RUNX1 regulates and thereby the expression of clinically important glycosphingolipids implicated in blood group incompatibility and host-pathogen interactions.