Polymorphic Alu are eQTLs at breast cancer risk loci. Loci, drawn to scale with the trait-associated SNPs (TAS) annotated, were edited by CRISPR to create cell lines that differed in genotype at the indicated Alu (red). qRT-PCR was performed on cell lines homozygous for the Alu insertion and lines homozygous for the absence of the Alu. Error bars are the standard deviation from 12 qRT-PCR measured ratios (two lines homozygous for the Alu relative to two lines homozygous for no Alu, each tested from two different cultures, in technical triplicate). (A) The presence of Alu-271 reduces PTHLH (red) expression. (B) The presence of Alu-098 increases RANBP9 (red) expression. (C) The presence of Alu-103 results in MYC (red) and PVT1 (blue) up-regulation compared to when Alu-103 is absent.
