There were 298 genotyped and imputed variants located in the SRE-5 chromosome 4 GWS region. Using matSpDlite (Li & Ji, 2005; Nyholt, 2004), the estimated number of effective tests was 132; therefore, the significance threshold for the fine mapping analysis was determined as P-value <3.79E-04. None of the variants tested individually reached this significance threshold. Table 3 lists all variants with P-values <0.01 in fine mapping; some, for instance, had P-values <0.01 in COGA but P-values >0.05 in NIAAA, possibly due to the much smaller sample size of the NIAAA cohort. These variants from both COGA and NIAAA had similar allele frequencies as the African sample in the genome aggregation database (genomAD, http://gnomad.broadinstitute.org/). However, they had dramatically different allele frequencies from the gnomAD non-Finnish European sample, indicating that they were ancestry informative, as expected. Carrying an effective allele increased SRE-5 scores (Table 3) and the effective allele frequencies were higher in Africans than in non-Finnish Europeans for all of these variants, except rs79462764. This was consistent with the results of admixture mapping. All variants in Table 3 individually had conditional
