In silico and in vitro DNA-protein binding studies. EMSA results, binding sequence motifs for each transcription factor and the DNA sequence around each SNP (alleles in red) are shown. Sequences are shown in the strand direction for which the prediction was found, and red underlines indicate homology between TF motif and allele sequence. DNA motifs were obtained from TRANSFAC and Schmidt et al. (C/EBPα) [12, 50]. Arrows indicate specific bands for each EMSA. (A) Both alleles of rs1799943 show weak in vitro binding of C/EBPα. (B) Analysis of rs9567576, using cell extract from two cell lines as indicated, and competition assays indicate stronger binding of HMGA1 to the probe containing the T allele. (C) EMSA analysis of rs4942485 for the A allele (upper panel) and G allele (lower panel). The A allele shows strong binding to DBP, as identified by competition assays. When using the probe containing the G allele, a lower third band appears in the presence of Zn2+ in the buffer, identified as binding to ZF5 in competition assays. EMSA, electrophoretic mobility shift assay; DBP, d-binding protein; SNP, single nucleotide polymorphism; TF, transcription factors.