Fig. 4

Relationships between genetic variants and retrotransposons. a Density distributions of different retrotransposon groups within (viz. at distance = 0 bp) or near SNPs, SIDs, and breakpoints of SCNVs, MCNVs, and LCNVs. Arrows on y-axes indicate autosomal averages of the retrotransposon group. b Distributions of genetic variants, recombination hotspots (Rec-H), recombination intensity (Rec), positive selection (PosSel) indicated by average |nSL| values, negative selection (NegSel) indicated by phyloP scores, as well as GWAS-identified SNPs both inside (at distance = 0 bp) and within ± 250 bp of different groups of SVAs, short interspersed nuclear elements (SINE), and long interspersed nuclear elements (LINE). Designations and numbers of the retrotransposon groups indicated at the top of the columns are color-coded based on their relative ages, ranging from red for the youngest to dark blue for the oldest. Colored asterisks mark significant enrichments (red) or depletions (blue) of features based on Monte Carlo simulations (n = 1000; *p < 0.005), and the dashed horizontal lines indicate the respective autosomal averages of each y-axis feature. c Density of long (MCNV, LCNV, ECNV, SDP) in the left panel, or short (SID, MST, SCNV) structural variations in the right panel, in vicinities of the younger (SVAs, AluYs, L1vy, L1y) or older (AluS, AluJ, FLAM, MIR, L1m, L1o, L2) retrotransposon groups. SV stands for structural variation; RE for retrotransposon; p value < 0.05 is shown in red (unpaired one-tailed t-tests). d Enrichment of y-axis genetic variants within ± 50 bp of x-axis genetic variants expressed by the thermal scale representing the natural-log of the density fold-change relative to the autosomal average