Pilot data from the 1000 Genomes Project (August 2010 haplotypes) was used to impute a 2Mb region surrounding the PYHIN1 gene in all studies using impute226. The EUR haplotypes (European) were used as a reference for the European American studies (assuming an effective population size [Ne] of 11418), the EUR and AFR (African) haplotypes were used as a reference for the African American studies (assuming Ne=15000), and the EUR, AFR, and ASN (Asian haplotypes) were used as a reference for the Latino studies (assuming Ne=15000). Individual genotypes were filtered for probabilities > 90%, and only SNPs with call rates > 90% were included in allelic tests of association. For family-based studies, SNPs with Mendelian errors were removed.
