Supplementary Figure 3: Comparison of imputation based on HapMap 2 and 1000 Genomes Project data.
From: An atlas of genetic influences on human blood metabolites
Correlation between (a) minor allele frequency (MAF) in meta-analysis, (b) association P value in meta-analysis (on a –log10 scale) and (c) average variance explained for the most significant SNPs selected from imputation based on either the HapMap 2 (x axis) or 1000 Genomes Project (y axis) panels. High correlations between the HapMap 2 and 1000 Genomes Project data sets support the view that metabolic associations are driven by common variants that are well tagged by HapMap 2 imputation. (d,e) One exception is the CYP3A4-CYP3A5-CYP3A7 locus where the 1000 Genomes Project scan reveals an additional variant (rs10278040) with greater association and variance explained for androsterone sulfate than for the corresponding HapMap 2 variant (rs148982377). (HapMap 2: rs148982377, MAF = 0.038, P = 7.65 ×10–244, R2 = 15.6%; 1000 Genomes Project: rs10278040, MAF = 0.042, P = 8.82 ×10–113,
= 10.3%.)
