We next focused on the ~100 kb linkage disequilibrium block containing the most significant SNPs, and determined whether other transcripts or functional elements are located in the block. By examining the UCSC Genome Browser annotations26, we did not identify predicted genes, predicted transcription start sites, spliced human expressed sequence tag (EST) sequences, known microRNA genes or predicted microRNA targets that overlap with the linkage disequilibrium block (Supplementary Fig. 5). However, we note that the linkage disequilibrium block contains several highly conserved genomic elements, including a 849-base pair (bp) element that ranks as the top 0.026% most-conserved elements in the entire human genome (log odds (LOD) score 5 3,480 by PhastCons27, Fig. 1b). Consistent with previous reports that large stable gene deserts typically contain regulatory elements for genes involved in development or transcription28, we hypothesized that these tagging SNPs were capturing the association of functional variants that regulate the expression and action of either CDH10 or CDH9.
