9cfd62d70caa8a7ce7610fcd55c1cf2cc6ef942b jnavarr5 Wed Feb 4 10:52:00 2026 -0800 Making lines less than 100 characters. Fixing typos from code review, refs #37057 diff --git src/hg/makeDb/trackDb/human/varFreqs.html src/hg/makeDb/trackDb/human/varFreqs.html index 6d672bc37cb..c86b4361e97 100644 --- src/hg/makeDb/trackDb/human/varFreqs.html +++ src/hg/makeDb/trackDb/human/varFreqs.html @@ -1,40 +1,42 @@

Description

This container shows results from projects where the variant frequencies, aka allele frequencies, are publicly available. The tracks were collected from the -projects listed below. More detailed data for projects that provide haplotype-phased genotypes/variants can also be found +projects listed below. More detailed data for projects that provide haplotype-phased +genotypes/variants can also be found in other tracks: 1000 Genomes is a separate track, and the projects HGDP, SGDP, -HGDP+1000 Genomes and Mexico Biobank can be found in the "Phased Variants" track, showing the linkage between variants. +HGDP+1000 Genomes and Mexico Biobank can be found in the "Phased Variants" track, showing +the linkage between variants.

If you want us to add other projects, please contact us. We were unable to obtain variant frequencies from the following projects: UK Biobank (request pending), Regeneron's Million Exomes and Mexico City Studies (request rejected).

The following projects were added:

Mexico City Prospective Study (MCPS): 9,950 whole genome sequenced individuals and 141,046 exome sequenced and genotyped individuals from the Mexico City Prospective Study (MCPS), a collaboration between the Regeneron Genetics Center, University of Oxford, Universidad Nacional Autónoma de México (UNAM), National Institute of Genomic Medicine in Mexico, Abbvie Inc. and - AstraZeneca UK. For details see (Ziyatdinov A, Nature 2023), the reference section. + AstraZeneca UK. For details, see (Ziyatdinov A, Nature 2023) in the reference section.
Regeneron Million Exomes Project (ME): Whole-exomes of 983,578 individuals sequenced by the Regeneron Genetics Center (RGC). These data span dozens of collaborations including large biobanks and health systems. All data were generated by the RGC on a single, harmonized sequencing and informatics protocol. The dataset includes individuals across diverse ancestral populations, encompassing outbred and founder populations and cohorts with high rates of consanguinity. See (Sun et al, Nature 2024) for details.
NHLBI TOPMED Freeze 10: @@ -46,31 +48,32 @@ disorders to advance precision medicine and improve population health. Freeze 10 contains 868,581,653 variants from 150,899 whole genomes. VCFs were downloaded from BRAVO.
SFARI SPARK: The Simons Foundation Autism Research Initiative (SFARI) recruited a large cohort of families with autistic children who provided DNA samples and phenotypes. 54,558 families, parents and their children were sequenced, a total of 142,357 individuals with whole-exome (WES) and 12,519 with whole-genome sequencing (WGS). The data contains 32,559 trios and 8,895 quads (one sibling without autism), and 824 twins. The same frequencies shown here - are also available publicly on the SFARI Genome Browser. + are also available publicly on the + SFARI Genome Browser. See (SPARK et al, Neuron 2018) for details or the methods below on this page.
GenomeAsia Pilot (GAsP): Whole-genome sequencing data of 1,739 individuals from 219 population groups across Asia. See (GenomeAsia Consortium, Nature 2019) for details.
Australia MGRB: The Australian Medical Genome Reference Bank collected whole-genome sequencing data of 4,011 healthy elderly individuals who @@ -85,126 +88,130 @@ The NCBI ALlele Frequency Aggregator pipeline computes allele frequencies from approved, unrestricted dbGaP studies and makes them publicly available through dbSNP. Its goal is to release frequency data from over one million dbGaP subjects to aid discoveries involving common and rare variants with biological or disease relevance. The R4 release includes 408,709 subjects and allele frequencies for 15.5 million rs sites, including nearly one million ClinVar variants. We converted the NCBI track hub to VCF format, the data is freely available. Genotype and associated individual-level data are accessible through the dbGaP authorized access request system.
FinnGen: Imputed variants from 500,348 Biobank samples obtained using genotyping arrays - in Finnland, 10% of the population. The imputation used phased variants obtained from 8,554 - high-quality whole genome sequences, also from Finnland. For details, see (Kurki et al, + in Finland, 10% of the population. The imputation used phased variants obtained from 8,554 + high-quality whole genome sequences, also from Finland. For details, see (Kurki et al, Nature 2023). Phenotype links can be shown at FinnGen PheWeb.
SweGen: Whole-genome sequencing variant frequencies for 1000 Swedish individuals generated within the SweGen project. The 1000 individuals included in the SweGen project represent a cross-section of the Swedish population and that no disease information has been used for the selection. The frequency data may therefore include genetic variants that are associated with, or causative of, disease. SweGen also provides SV calls, TEs, MELT results for TEs, HLAs and new sequence. For details, see (Ameur et al, Eur J Hum Genet 2017). - Dataset can be browsed at the + The dataset can be browsed at the SweGen Browser.
JPN To61k Japan Tohoku University Tohoku Medical Megabank Organization 61k Allele frequency panel (JPN 61k): An allele frequency panel based on short-read WGS analysis of 61,000 Japanese individuals. The project includes other datatypes, such as STRs, long-read SVs and short-read CNVs. Data can be downloaded from the jMorp Website, specifically the Downloads section. For details, see (Tadaka et al, NAR 2023).
Brazil Arquivo Brasileiro Online de Mutaçõ (ABraOM): Genomic variants obtained with whole-genome sequencing from SABE, a census-based sample of elderly individuals from São Paulo, Brazil's largest city. The Brazilian population is constituted by ~500 years of admixture between Africans, Europeans, and Native Americans. Additionally, the cohort presents ~3% of individuals with non-admixed Japanese ancestry (early 20th century migration). Coverage 38.6x. Data can be downloaded from the AbraOM Website. TEs, HLAs and new sequence are also available. - For details see (Naslavsky et al, Nat Comm 2022). + For details, see (Naslavsky et al, Nat Comm 2022).
IndiGenomes: Whole genome sequencing of 1,029 healthy Indian individuals under the pilot phase of the "IndiGen" program. Data can be downloaded from the IndiGen Website. For details see (Jain et al, NAR 2020). Only + target="_blank">IndiGen Website. For details, see (Jain et al, NAR 2020). Only the allele frequency is available from this project. The website also provides SV call and Alu insertion VCFs.
Korean Variant Archive (KOVA): 1,896 whole genome sequencing and 3,409 whole exome sequencing data from healthy individuals of Korean ethnicity. Most of the samples originated from normal tissue of cancer patients (40.16 %), healthy parents of rare disease patients (28.4 %), or healthy volunteers (31.44 %). Japanese ancestry is broken down in the INFO field. Coverage 100x for WES, 30x for WGS. SVs called with Manta - are also available. For details see (Lee et al, Exp Mol Med 2022).
NPM Singapore: 9,770 whole genomes, mostly of Chinese, Indian and Malay ancestry. A minimum allele count cutoff of > 5 was applied. Data is available for download from the CHORUS browser, see "Data access" below. - For details see (Wong et al, Nat Genetics 2023). CNV data is also available there. + For details, see (Wong et al, Nat Genetics 2023). CNV data is also available there.
Saudi Genome Program: Variant frequencies from 302 whole genomes at 30x coverage, on Saudi Genome Program Samples. The genotyping data and imputations from 3,352 individuals do not seem to be available - publicly. For details see (Malomane et al 2025). + publicly. For details, see (Malomane et al 2025).

Display Conventions

Most tracks only show the variant and allele frequencies on mouseover or clicks. When zoomed in, tracks display alleles with base-specific coloring. Homozygote data are shown as one letter, while heterozygotes will be displayed with both -letters. All VCF files are normalized, with one single allele per annotation (no multi-allele lines). +letters. All VCF files are normalized, with one single allele per annotation (no multi-allele +lines).

Data Access

Most of the data in these tracks are not available for download from UCSC and the data can only be browsed on our website. -But all variant data can be downloaded for free from the original project websites. Accessing it usually requires a click-through license or filling out an access request form on the respective websites, by following these instructions: +

+Most of the data in these tracks are not available for download from UCSC and the data can only be +browsed on our website. But all variant data can be downloaded for free from the original project +websites. Accessing it usually requires a click-through license or filling out an access request +form on the respective websites, by following these instructions:

MXB: Allele frequencies by geographical state and ancestry are available via the MexVar platform. Raw genotype data are available under controlled access at the EGA (Study: EGAS00001005797; Dataset: EGAD00010002361). For the VCFs, email andres.moreno@cinvestav.mx.