Effect of retrotransposon eQTLs on gene expression.

Retrotransposon polymorphisms were correlated with gene expression from microarray dataset E-MTAB-197. The top significant effects after FDR correction are presented. Gene: Gene within which the polymorphism occurred and whose expression is correlated with the presence/absence of the polymorphism; Retrotransposon: Polymorphic retrotransposon identified by the 1000 genomes project; Variant: Noted as the presence or absence versus the reference genome; Effect: The effect was calculated by regressing variant status on normalized microarray expression level; rho: Spearman's rank correlation rho was calculated for each comparison; p : raw p-value from Spearman's rank correlation; AF: Allele frequency in given populations;*denotes values which are taken directly from 1000 genomes data [35].