Affymetrix 6.0 genotyping and QC filtering of African-American samples from the CARe cardiovascular consortium was performed as described previously50. After QC filtering for each of ARIC, CARDIA, CFS, JHS and MESA cohorts and subsequent merging, 8,367 samples and 770,390 SNPs remained. To limit relatedness among samples we restricted all analyses to a subset of 5,129 samples in which all pairs have genome-wide relatedness of 0.05 or less and had between 5% and 45% European ancestry. We performed local ancestry inference using the HAPMIX software with the CEU and YRI HapMap populations as reference ancestral populations. We examined seven phenotypes from the CARe cohort, height, body mass index (BMI), log transformed high density lipoprotein cholesterol (logHDL), low density lipoprotein cholesterol (LDL), white blood cell count (WBC), diastolic blood pressure (DBP), and systolic blood pressure (SBP). For each phenotype we included age, sex, study center, proportion of European ancestry, and the top 5 principal components as fixed effects. A detailed description of the phenotypes can be found here51.
