Preferential binding of FOXA1 at a heterozygous SNP. SNP rs7248104 is located in a FOXA1 binding sequence and FOXA1 is preferentially bound to one allele. At the top is the FOXA1 motif, predicted by the BCRANK method, followed by the sequence found in HepG2 with the alleles of the heterozygous SNP (T/C) in brackets. These are followed by the sequence in the reference genome and the sequence found in the FOXA1-reads. At the SNP position, the T-allele corresponds to the FOXA1 motif, which is found in all 15 FOXA1 reads, while the C-allele in the reference genome is not detected at all. The raw data for individual FOXA1 reads in the region are presented at the bottom, viewed in the SOLiD™ Alignment Browser tool. The positions marked in green correspond to bases (in the SOLiD™ two-base encoding) that align to the reference genome. In gray are the bases with a match error. The yellow bases correspond to positions with valid adjacent mismatches, indicating the locations of SNPs. The vertical hatched lines enclose the position of the motif.
Motallebipour et al. Genome Biology 2009 10:R129 doi:10.1186/gb-2009-10-11-r129