VarGen is an R package designed to get a list of variants related to a disease. It just need an OMIM morbid ID as input and optionally a list of tissues / gwas traits of interest to complete the results. You can also use your own customised list of genes. VarGen is capable of annotating the variants to help you identify the most impactful ones.
Due to a change in biomaRt, _get_phenotypeterms() does not return a list of phenotypes anymore.
obesity_phens <- get_phenotype_terms(keyword = "obesity", snp_mart = snp_mart)However, _get_variants_fromphenotypes() still works if the user knows the list of phenotypes to use as input.