Affymetrix 6.0 genotyping and QC filtering of African-American samples from the Women's Health Initiative (WHI) SNP Health Association Resource (SHARe) was performed as described previously52. The dataset includes extensive phenotypic and genotypic data on 12,008 African American and Hispanic women aged 50-79 enrolled in one or more components of the WHI program. We included only African American samples and to limit relatedness among samples we restricted all analyses to a subset of 8,153 samples in which all pairs have genome-wide relatedness of 0.05 or less. We performed local ancestry inference using the SABER+23 software with the CEU and YRI HapMap populations as reference ancestral populations. We examined 10 phenotypes from the WHI cohort (BMI), log transformed high density lipoprotein cholesterol (logHDL), low density lipoprotein cholesterol (LDL), white blood cell count (WBC), log transformed triglycerides (logTG), glucose, log transformed insulin (logInsulin), QT interval duration (QT-INTERVAL), C-reactive protein (CRP), diastolic blood pressure (DBP), and systolic blood pressure (SBP). For each phenotype we included age and proportion of European ancestry as fixed effects. A detailed description of the phenotypes can be found here52.
