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Across many species, a large fraction of genetic variants that influence phenotypes of interest is located outside of protein-coding genes, yet existing methods for identifying such variants have poor predictive power. Here, we introduce a new computational method, called LINSIGHT, that substantially improves the prediction of noncoding nucleotide sites at which mutations are likely to have deleterious fitness consequences, and which therefore are likely to be phenotypically important. LINSIGHTdoi:10.1038/ng.3810 pmid:28288115 pmcid:PMC5395419 fatcat:taxvf6jg3nat7k5t2w3spkmv6m