National/ethnic variation databases | Genome annotation

Expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups.

Offers genome structural information pertaining to Asian populations in a familiar graphical comparative view. PanSNPdb offers pre-computed information of linkage disequilibrium (LD) blocks and their haplotypes on each chromosome. The comprehensive information in this database can be considered as worldwide data collection, but with special emphasis on Asian populations. The Haploview tool is also integrated into the PanSNPdb website: users can adjust the haplotype inferencing parameters in order to recalculate haplotype blocks ‘‘on-the-fly’’.

Provides re-analyzed genotyping and next generation sequencing (NGS) data sets. PGG.Population permits understanding the genomic diversity and genetic ancestry of human populations. It contains a comprehensive description of the genomic diversity of over 350 population, including their genetic affinity, population structure, genetic admixture, ancestral architecture, and footprints of natural selection in their genomes.

Provides information on the occurrence of genetic disorders in the Arab populations. Information in CTGA is drawn from published research and mined hospital records. The database offers web-based basic and advanced search approaches. In either case, the final search result is a detailed HTML record that includes text-, URL- and graphic-based fields.

Offers experimental details and marker information allelotyped in population of Taiwan. TPMD is a shared database and resources for genotyping with microsatellite markers that reduces cost and errors of genotyping and facilitates disease gene mapping in human populations. This resource contains two major sections including the database for sharing useful microsatellite marker information and the resources for supporting consistent genotyping experiments.