Closer examination of the 5p14.1 region indicated that all genotyped and imputed SNPs with P values below 1 × 10−7 reside within the same ~100 kilobase (kb) linkage disequilibrium block, suggesting that these SNPs are tagging the same variants (Supplementary Figs 1 and 2). The linkage disequilibrium block is located within a 2.2-megabase (Mb) intergenic region between CDH10 (cadherin 10) and CDH9 (cadherin 9) (Fig. 1b, c). Both CDH10 and CDH9 encode type II classical cadherins from the cadherin superfamily, which represent transmembrane proteins that mediate calcium-dependent cell-cell adhesion. To search for other types of variants, including copy number variations (CNVs), in the intergenic region, we used the PennCNV software25 on the signal intensity data and identified five CNV loci (Supplementary Fig. 3). All of these CNVs are present in control subjects in our study, and three of the five CNVs are also reported in the Database for Genomic Variants that annotates healthy individuals (Supplementary Fig. 4), suggesting that CNVs in the region are unlikely to be causal variants for ASDs.
