SNP-based heritability, genetic correlation estimation, and partitioned heritability analyses were performed using the LD score approach [39] (scripts available at https://github.com/bulik/ldsc). Partitioned heritability was performed to examine enrichment of the heritability estimates within SNPs annotated per functional classes based on gene structure (promoter, intron, coding, UTR) and regulatory elements (Histone and DNASE-I hypersensitivity sites). We also examined cell type-specific histone binding elements to identify whether enrichment was limited to specific cell and tissue types. Finally, we applied the partitioned heritability method to examine whether enrichment existed in genes and gene-pathways previously implicated in ASD (see Additional file 1).
