+ rs4986893, a CYP2C19 stop-gained variant common in + East Asian populations. The mouseover ranks ToMMo Japan, KOVA Korea, and WBBC + China at the top, well above the 1.6% pooled background AF.
+You can sign-up to get these announcements via our Genome-announce email list. We send around one short announcement email every two weeks.
Smaller software changes are not announced here. A summary of the three-weekly release changes can be found here. For the full list of our daily code changes head to our GitHub page. Lastly, see our credits page for acknowledgments of the data we host.
+ ++We are pleased to announce a new +SNV +Frequencies supertrack on the human assembly (GRCh38/hg38). The +collection unifies single-nucleotide variant allele frequencies from 30+ +population resequencing and biobank projects worldwide, covering roughly +1.7 million genomes, exomes, and genotyping arrays, into a single place +where a variant's frequency can be compared across populations, ancestries, +and disease cohorts. +
+ ++The collection includes three combined tracks that aggregate the source +data along different lines: +
+
+ rs4986893, a CYP2C19 stop-gained variant common in + East Asian populations. The mouseover ranks ToMMo Japan, KOVA Korea, and WBBC + China at the top, well above the 1.6% pooled background AF.
++Each variant in the combined tracks is colored by predicted protein +consequence +(loss-of-function, +missense, +synonymous, +non-coding), and +carries pooled allele counts and pooled allele frequencies (sum AC / sum +AN) across the contributing cohort arms. Cross-database filters allow +you to narrow to variant type, consequence, source database, length, or +any combination of per-track AC/AF/AN ranges. +
+ ++The supertrack pulls together cohorts from across the world. A high-level +summary of the regions and contributing projects is shown below; a +complete table with per-cohort sample counts, data types, sub-populations +and download status is on the +supertrack +description page. +
+ +| Region | Contributing cohorts |
|---|---|
| East Asia | ToMMo, GenomeAsia, NPM, KOVA, WBBC, ChinaMAP, TPMI |
| South Asia | IndiGen, GenomeIndia |
| Africa | Tishkoff |
| Americas | AllOfUs, TOPMed, ABraOM, Mexico Biobank |
| Europe | FinnGen, SweGen, GoNL, HRC, UK Biobank, ALFA |
| Middle East | Saudi |
| Oceania | MGRB |
| Disease cohorts | SFARI SPARK (WES + WGS), SCHEMA, GREGoR, GA4K |
| Global reference panels | SGDP, gnomAD HGDP+1kG |
| Long-read / linked-read | GA4K, CoLoRSdb, SVatalog |
+License restrictions on some sources limit redistribution; see the +supertrack description page for per-cohort details. +
+ ++We plan to continue updating this track as more population-scale +allele-frequency datasets become available. If you are involved with a +project that publishes variant frequencies and would like to contribute, +please reach out. +
+ ++We would like to thank the millions of participants worldwide who donated +samples and shared health information to make this data possible; the +investigators who provided the variant files, including Matthew Hansen +(Tishkoff lab), Insoo Jang (KOVA), and Andreas Lahner (MGZ) for feedback; +and Alex Ioannidis (UCSC) for the motivation behind the track. The track +was developed by Maximilian Haeussler with QA and review by Lou Nassar. +
+We are happy to announce release 3 of the Varaico Variants and Varaico Variants (suppl) tracks for the human assemblies hg38/GRCh38 and hg19/GRCh37. This release contains a precision improvement and an update of the underlying literature. The Varaico tracks are created using literature mining, similar to AVADA.
The Varaico Variants (suppl) track contains variants extracted from supplementary data files using similar methods as in the Varaico track. The previous (release 2)