details of mgs subject recruitment and sample characteristics are provided in the online full methods ( section a1 ) .
samples ( 5.3% ) were excluded for high missing data rates , outlier proportions of heterozygous genotypes , incorrect sex or genotypic relatedness to other subjects .
snps ( 7% for african american , 25% for european - ancestry and 27% for combined analyses ) were excluded for minor allele frequencies less than 1% , high missing data rates , hardy - weinberg deviation ( controls ) , or excessive mendelian errors ( trios ) , discordant genotypes ( duplicate samples ) or large allele frequency differences among dna plates .
principal component scores reflecting continental and within - europe ancestries of each subject were computed and outliers excluded .
genomic control  values for autosomes after qc were 1.042 for african american and 1.087 for the larger european - ancestry and combined analyses . for mgs ,
association of single snps to schizophrenia was tested by logistic regression ( trend test ) using plink10 , separately for european - ancestry , african american and combined datasets , correcting for principal component scores that reflected geographical gradients or that differed between cases and controls , and for sex for chromosome x and pseudoautosomal snps .
genotypic data were imputed for 192 regions surrounding the best findings , and for additional regions selected for meta - analysis.11 detailed results are available in supplementary datafiles 1 and 2 , and complete results from dbgap ( www.ncbi.nlm.nih.gov/sites/entrez?db=gap ) .
meta - analysis of the mgs , isc and sgene datasets was carried out by combining p - values for all snps ( in the selected regions ) for which genotyped or imputed data were available for all datasets , with weights computed from case - control sample sizes .
 schizophrenia , a devastating psychiatric disorder , has a prevalence of 0.51% , with high heritability ( 8085% ) and complex transmission.1 recent studies implicate rare , large , high - penetrance copy number variants ( cnvs ) in some cases2 , but it is not known what genes or biological mechanisms underlie susceptibility . here 
 we show that schizophrenia is significantly associated with single nucleotide polymorphisms ( snps ) in the extended major histocompatibility complex ( mhc ) region on chromosome 6 . 
 we carried out a genome - wide association study ( gwas ) of common snps in the molecular genetics of schizophrenia ( mgs ) case - control sample , and then a meta - analysis of data from the mgs , international schizophrenia consortium ( isc ) and sgene datasets . 
 no mgs finding achieved genome - wide statistical significance . in the meta - analysis of european - ancestry subjects ( 8,008 cases , 19,077 controls ) , significant association with schizophrenia 
 was observed in a region of linkage disequilibrium on chromosome 6p22.1 ( p = 9.54  109 ) . 
 this region includes a histone gene cluster and several immunity - related genes , possibly implicating etiologic mechanisms involving chromatin modification , transcriptional regulation , auto - immunity and/or infection . 
 these results demonstrate that common schizophrenia susceptibility alleles can be detected . 
 the characterization of these signals will suggest important directions for research on susceptibility mechanisms . 
Methods summary
Supplementary Material