Overall, there were no compelling results in these sets (all P > 10−4), considering the number of SNPs tested, and only two regions met criteria for region-wide (only SNPs in that gene/region considered) or set-wide (e.g. all candidate regions in the set of common variant genes considered) significance by permutation-testing (Supplementary Table 5). MECP2 (Rett syndrome) met criteria for region-wide association (P = 0.0071, 5 SNPs, Supplementary Table 5). Moreover, the Williams syndrome region was borderline for set-wide significance (P = 0.051, Supplementary Table 5). One SNP in particular showed strong association (rs2267831, P = 0.00012, OR = 0.56) – as this was a rare SNP with undertransmission of the minor allele, we genotyped a subset of families and observed similar, slightly less significant distortion (OR=0.61). The SNP is located within GTF2IRD1, a transcription factor within the critical region for the Williams syndrome cognitive behavioral profile 9,10,11.
