Warfarin is the most commonly used oral anticoagulant for thrombotic disorders and atrial fibrillation. The dose is influenced by CYP2C9 and VKORC1. CYP2C9 variants change the protein sequence, but VKORC1 variants are non-coding and thought to act through regulation of gene expression. Which VKORC1 variant that mediates the effect has not been resolved due to high linkage disequilibrium (LD). We used ENCODE data on regulatory transcription factor binding sites, and heterozygous positions in a liver cell line to determine variants that regulate VKORC1. We sequenced the liver cell line HepG2 to locate all heterozygous positions in LD r2>0.8 with the GWAS top hits, and used ENCODE data to find variants that bind transcription factors in an allele-specific way. The functional effect of these variants was evaluated using luciferase assays and over-expression of candidate transcription factors. VKORC1 rs9923231 was not located in an ENCODE regulatory element, and luciferase assays did not show any difference in transcriptional activity between the two alleles. One allele-specific SNP, rs56314408, was on the same haplotype as rs9923231, and rs2032915 was located in the same liver enhancer 24 bp away. The C alleles of rs56314408 and rs2032915 showed higher transcriptional activity, which was further increased after over-expression of the transcription factors YY1 and USF1. We are currently evaluating the potential regulatory effect of rs56314408 and rs2032915 using CRISPR/Cas9. The conventionally analyzed VKORC1 -1639 G>A (rs9923231) is not located in a regulatory element in the liver, and has no evidence of being functional. The LD between rs9923231 and both functional candidates rs56314408 and rs2032915 is known to be high in Europeans. We propose that rs9923231 predicts warfarin dose adequately only in populations where it is in high LD with functional variants such as the candidates rs56314408 and rs2032915.