Data from: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

Variation in the presence or absence of transposable elements (TEs) is a major source of genetic variation between individuals. Here, we identified 23,095 TE presence/absence variants between 216 Arabidopsis accessions. Most TE variants were rare, and we find these rare variants associated with local extremes of gene expression and DNA methylation levels within the population. Of the common alleles identified, two thirds were not in linkage disequilibrium with nearby SNPs, implicating these variants as a source of novel genetic diversity. Many common TE variants were associated with significantly altered expression of nearby genes, and a major fraction of inter-accession DNA methylation differences were associated with nearby TE insertions. Overall, this demonstrates that TE variants are a rich source of genetic diversity that likely plays an important role in facilitating epigenomic and transcriptional differences between individuals, and indicates a strong genetic basis for epigenetic variation.,Figure 2 - source data 3Arabidopsis TE variants, including final classifications for each variant as a TE insertion, deletion, or NA.TEPID_TEPAV.tsv.gzFigure 1 - source data 1TE insertions in Lerinsertions_ler.bed.gzFigure 1 - source data 2TE absences in Lerdeletions_ler.bed.gzFigure 2 - source data 1TE insertions in all 216 Arabidopsis accessionsinsertions.tsv.gzFigure 2 - source data 2TE absences in all 216 Arabidopsis accessionsabsences.tsv.gzFigure 2 - source data 4TE family enrichments for TE insertion and TE deletion variantsfamily_enrichments.tsvFigure 4 - source data 1Significantly differentially expressed genes dependent on TE presence/absencesig_genes.tsv,