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Although lysyl oxidase-like 1 ( LOXL1 ) is known as the principal genetic risk factor for pseudoexfoliation (PEX) syndrome, a major cause of glaucoma and cardiovascular complications, no functional variants have been identified to date. Here, we conduct a genome-wide association scan on 771 German PEX patients and 1,350 controls, followed by independent testing of associated variants in Italian and Japanese data sets. We focus on a 3.5-kb four-component polymorphic locus positioned spanning introns 1 and 2 of  LOXL1  with enhancer-like chromatin features. We find that the rs11638944:C>G transversion exerts a  cis -acting effect on the expression levels of  LOXL1 , mediated by differential binding of the transcription factor RXRα (retinoid X receptor alpha) and by modulating alternative splicing of  LOXL1 , eventually leading to reduced levels of  LOXL1  mRNA in cells and tissues of risk allele carriers. These findings uncover a functional mechanism by which common noncoding variants influence  LOXL1  expression.

Pseudoexfoliation syndrome-associated genetic variants affect transcription factor binding and alternative splicing of LOXL1