Schema for OMIM Pheno Loci - OMIM Phenotypes - Gene Unknown
  Database: hg38    Primary Table: omimLocation    Row Count: 1,196
Format description: Browser extensible data
fieldexampleSQL type info description
bin 0smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 0int(10) unsigned range Start position in chromosome
chromEnd 123400000int(10) unsigned range End position in chromosome
name 605606varchar(255) values Name of item

Sample Rows

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

OMIM Pheno Loci (omimLocation) Track Description


OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the OMIM database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. Further, please be sure to click through to for the very latest, as they are continually updating data.

OMIM is the property of Johns Hopkins University and is not available for download or mirroring by any third party without their permission. Please see OMIM for downloads.

OMIM is a compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known Mendelian disorders and over 12,000 genes. OMIM is authored and edited at the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, under the direction of Dr. Ada Hamosh. This database was initiated in the early 1960s by Dr. Victor A. McKusick as a catalog of Mendelian traits and disorders, entitled Mendelian Inheritance in Man (MIM).

The OMIM data are separated into three separate tracks:

OMIM Alleles
    Variants in the OMIM database that have associated dbSNP identifiers. This track is currently unavailable on the hg38 assembly, as it depends on dbSNP data that has not been released yet.

OMIM Genes
    The genomic positions of gene entries in the OMIM database. The coloring indicates the associated OMIM phenotype map key.

OMIM Phenotypes - Gene Unknown
    Regions known to be associated with a phenotype, but for which no specific gene is known to be causative. This track also includes known multi-gene syndromes.

This track shows the cytogenetic locations of phenotype entries in the Online Mendelian Inheritance in Man (OMIM) database for which the gene is unknown.

Display Conventions and Configuration

Cytogenetic locations of OMIM entries are displayed as solid blocks. The entries are colored according to the OMIM phenotype map key of associated disorders:

  • Lighter Green for phenotype map key 1 OMIM records - the disorder has been placed on the map based on its association with a gene, but the underlying defect is not known.
  • Light Green for phenotype map key 2 OMIM records - the disorder has been placed on the map by linkage; no mutation has been found.
  • Dark Green for phenotype map key 3 OMIM records - the molecular basis for the disorder is known; a mutation has been found in the gene.
  • Purple for phenotype map key 4 OMIM records - a contiguous gene deletion or duplication syndrome; multiple genes are deleted or duplicated causing the phenotype.

Gene symbols and disease information, when available, are displayed on the details pages.

The descriptions of OMIM entries are shown on the main browser display when Full display mode is chosen. In Pack mode, the descriptions are shown when mousing over each entry. Items displayed can be filtered according to phenotype map key on the track controls page.


This track was constructed as follows:

  • The data file genemap.txt from OMIM was loaded into the MySQL table omimGeneMap.
  • Entries in genemap.txt having disorder info were parsed and loaded into the omimPhenotype table. The phenotype map keys (the numbers (1)(2)(3)(4) from the disorder columns) were placed into a separate field.
  • The cytogenetic location data (from the location column in omimGeneMap) were parsed and converted into genomic start and end positions based on the cytoBand table. These genomic positions, together with the corresponding OMIM IDs, were loaded into the omimLocation table.
  • All entries with no associated phenotype map key and all OMIM gene entries as reported in the "OMIM Genes" track were then excluded from the omimLocation table.


Thanks to OMIM and NCBI for the use of their data. This track was constructed by Fan Hsu, Robert Kuhn, and Brooke Rhead of the UCSC Genome Bioinformatics Group.


Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM®). Nucleic Acids Res. 2009 Jan;37(Database issue):D793-6. Epub 2008 Oct 8.

Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D514-7.