The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome

(A) Chromosome 21–wide Manhattan plot and (B) Q–Q plot of SNP genotypic association test P-values for 187 DS-CHD and 151 DS-without CHD using 7238 SNPs on chromosome 21. (Red line) The Bonferroni threshold for chromosome 21–wide α = 0.05. SNPs are plotted in megabases relative to their position on chromosome 21. Two SNPs within the same LD block (r² = 1) reached chromosome 21–wide significance (P ≤ 0.05) (for details, see Table 1). (C) Regional association plot for the region identified to associate with DS-CHD. The panel shows the recombination rate in the region estimated from HapMap CEU data (http://hapmap.ncbi.nlm.nih.gov/), pairwise LD between SNPs in the region and the SNP identified (purple), and P-values for strength of associations and genes in the region. The r² values are color-coded according to the scale on the panel.