We attempted to replicate the associations reported in Supplementary Table 3 in the SHIP and SHIP-TREND cohorts23. The SHIP samples were genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0. The SHIP-TREND samples was genotyped using the Illumina Human Omni 2.5 array. Prior to imputation, duplicate samples (by IBS), samples with reported vs. genotyped gender mismatch or samples with a very high heterozygosity rate were excluded. Additionally, all monomorphic SNPs, SNPs with duplicate chromosomal position, SNPs with pHWE <0.0001 and SNPs with a callrate <95% were filtered. Imputation was performed on the Sanger Imputation Service (see URLs) against the HRC panel. In total, 4,070 SHIP samples and 986 SHIP-TREND samples were included in the imputation of genotypes. Association analyses were conducted using SNPTEST v2.5.224.
