rs1322784, an intragenic SNP associated with the 'disrupted in schizophrenia' DISC1 gene, was reported to be associated with asperger's syndrome [PMID 17579608]
This same study also implicated the "HEP3 haplotype" in asperger's syndrome. The HEP3 haplotype contains two SNPs in the DISC1 gene, rs751229 and rs3738401, and was first reported as a haplotype under-represented in individuals with affective disorders. [PMID 14532331, PMID 15386212]
[PMID 19414483] The DISC locus and schizophrenia: evidence from an association study in a central European sample and from a meta-analysis across different European populations.