Functional SNPs recapitulate the CTCF binding motif.

<p>(A) 4,428 SNPs identified by resequencing at as many sites. Y-axis indicates the number of SNPs identified at a given position (x-axis) relative to the aligned and strand-oriented CTCF motif (below). Bar color indicates alleles of SNPs. Gray shading indicates the 44-bp extent of protein-DNA interaction. Note that SNPs are uniformly distributed throughout the entire window, except for a slight reduction in diversity corresponding to the high-information content positions of the motif. (B) Of the SNPs in (A), 218 are significantly associated with ChIP-seq occupancy (FDR 1%). Color indicates SNPs for which the higher-occupancy allele (according to association analysis) also had a higher log-odds score in the known motif. Gray indicates SNPs that affected occupancy, but the higher-occupancy allele had a lower score in the motif. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002599#pgen.1002599.s002" target="_blank">Figure S2C</a> for full color. Note that these SNPs are concentrated in the region of protein-DNA contact, and 84% match the allele predicted by the canonical motif (above).