VSEA estimates the enrichment of overlap between genetic variants and genomic regions. It does this by selecting matched control variants and estimate the odds ratio between the probability of overlap between the foreground variants and genomic regions and that of the background variants. To account for LD, VSEA selects LD proxies based on 1000 Genomes phase 3 data. VSEA takes as input a set of genetic variants, and a set of genomic regions. It outputs the enrichment, standard error of the enrichment, and enrichment P-value.
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