GWAS often omit the X chromosome (chrX). This omission is problematic as chrX is approximately as large as chromosome 8 and is enriched for genes important in brain development. Using a previously described approach, we imputed genotyped chrX SNPs to the 1000 Genomes reference panel. 23 Joint analysis of all subjects as well as males and females separately revealed no association exceeding genome-wide significance. The strongest association (rs12845396, chrX:6,029,533, P=3.46×10−7) was in an intron of NLGN4X (neuroligin 4), a gene previously implicated in mental retardation and autism, and there were multiple possible signals nearMECP2(causal to Rett syndrome, P=9.3×10−6).
