Motifs are most enriched around the summits of DNase-seq peaks. a Aggregate motif density plots of 3kbp sequences centered on DNase-seq peak summits within SEs or TEs. Line plots are colored as in the enhancer class key in Figure 1. Cell-specific motif sets are generated by selecting motifs that are significantly enriched in SE DHS sequences and correspond to TFs that are significantly expressed. Individual motif density plots are generated by the Homer annotate Peaks tool  with motifs called at a threshold of 40% of the maximum log likelihood score. These individual motif density plots are summed together position-wise to generate the aggregate motif density plots (“Methods”). Motif densities are generally similar between the SE and TE sequences. b UCSC Genome browser view of the ZBED3-AS1 locus. Motif density tracks (Upper) identify portions of the genome assigned an enhancer state that are relatively rich in motifs. These tracks measure the number of non-overlapping motif sites in 150 bp windows at 10 bp steps and are auto-scaled for each cell type. Potentially functional SNPs that overlap SEs may not overlap any DHS, but may overlap portions of the SEs that are dense in motifs, such as the rightmost T2D tightly linked SNP. Chromatin state colors and scales for the other tracks are assigned as in Figure 1a. The black box highlights a strong overlap of cell-specific accessible chromatin and enhancer chromatin states that is also dense in motifs. These tracks are downloadable at http://fusion.nhgri.nih.gov/files/se-motifs/motifsBedgraphs.tar.