The total number of trait influencing variants is estimated as Mπ1, where M = 9,997,231 gives the number of SNPs in the reference panel. MiXeR Venn diagrams report the effective number of influencing variants, ηMπ_1, where η is a fixed number, η = 0.319, which gives the fraction of influencing variants contributing to 90% of trait’s heritability (with rationale for this adjustment being that the remaining 68.1% of influencing variants are small and cumulatively explain only 10% of trait’s heritability). Phenotypic variance explained on average by an influencing genetic variant is calculated as H_σβ2, where H_=1M∑iHi=0.2075 is the average heterozygosity across SNPs in the reference panel. Under the assumptions of the MiXeR model, SNP-heritability is then calculated as hSNP2=Mπ1×H_σβ2.
