description: We systematically assess whether variants in inaccessible regions are underrepresented on genotyping chips and imputation reference panels, in the GWAS catalog and in the ClinVar database. We also determine the proportion of genes located in inaccessible regions and compare the results across inaccessibility masks defined by the 1000 Genomes Project and the TOPMed program. Results Fewer variants were observed in inaccessible regions in all analyzed categories. Depending on the mask and normalized for region size, only 4-17% of the genotyped variants are located in inaccessible regions and 52 to 581 genes were almost completely inaccessible. From the Cooperative Health Research in South Tyrol (CHRIS) study, we present a case study of an association located in an inaccessible region that can only be identified with genotyped variants in GRCh37 since imputation was inaccurate. To facilitate researchers assessing gene and variant accessibility easily, we provide an online application (https://gab.gm.eurac.edu). Genotyping, NGS, genotype imputation and downstream applications such as GWAS and fine mapping are systematically biased in inaccessible regions, due to spurious associations and missed variants.