Figure 2

Genomic location and evolutionary conservation of noncoding variants. (A) The genomic position of highly conserved noncoding single nucleotide variants (SNVs) in NLGN3 overlap with H3K4Me1 enhancer- and promotor-associated marks in various cell types (orange = H1 embryonic stem cells, green = human mammary epithelial cells (HMEC) and purple = human leukemia cells (K562)); CD34 cells nuclease accessibility sites (NAS) (purple = sites on CD34+ cells and blue = sites of CD34- cells); and human-mouse-rat (HMR) conserved transcription factor binding sites (TFBS) (orange blocks). The two variants that fall within HMR TFBS are highlighted in green. (B) Variant (chrX:70291656; also outlined in a green box) is located within a highly conserved 15-bp Bach1 TFBS (z-score 2.86, P < 0.003;). The sequence logo for the consensus Bach1 TFBS is shown to the right. The black arrow shows the position of the the variant (chrX:70291656) within this highly conserved binding motif. (C) Variant (chrX:70284973; outlined in a green box) is located within a highly conserved 14-bp Roaz TFBS (z- score 2.86, P < 0.003). The sequence logo for the consensus Roaz TFBS is shown to the right. The black arrow shows the position of the the variant (chrX:70284973) within this highly conserved binding motif.