89491842e0ec6b2250aa6f6dc2c83c294930e6d6 max Sun May 17 14:38:40 2026 -0700 Add ChinaMAP phase 1 variant frequencies subtrack on hg38 ChinaMAP (Cao et al. 2020, Cell Res, PMID 32355288) is a deep-WGS cohort of 10,588 Chinese individuals across 27 provinces and 8 ethnic groups, with 147.4 M autosomal variants (136.7 M SNPs + 10.7 M short indels). The released VCF is already on GRCh38 with chr-prefixed chromosomes and ships AC/AF/AN plus matched 1KGP_* INFO fields, so it is served directly via vcfTabix. The ChinaMAP Limitations on Use prohibit redistribution, so the gbdb directory is _chinamap (hidden from hgdownload) and the trackDb stanza has tableBrowser off. Registered in scripts/varFreqs/databases.tsv so the next varFreqsAll combined rebuild picks it up; filter UI is deliberately not added yet (WBBC/TPMI precedent). , refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra index 2bb10d09a3a..e746bcd3e2c 100644 --- src/hg/makeDb/trackDb/human/varFreqs.ra +++ src/hg/makeDb/trackDb/human/varFreqs.ra @@ -1,600 +1,611 @@ track varFreqs shortLabel Variant Frequencies longLabel Variant Frequencies from various cohorts or national projects group varRep type bed 12 visibility hide superTrack on track varFreqsAll shortLabel All Databases Combined longLabel Variant Frequencies: All Databases Combined with Consequence Annotations type bigBed 9 + parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_all/varFreqsAll.bb visibility pack itemRgb on maxWindowToDraw 5000000 priority 0.1 mouseOver Var: $name
AA change: $aaChange
Var type: $varType
Conseq: $consequence
Max AF: $maxAF
Total AC: $totalAC
Sources: $sources # Variant type and consequence filters filterValues.varType SNV|SNV,INS|Insertion,DEL|Deletion,MNV|MNV filterLabel.varType Variant Type filterValues.consequence missense|Missense,synonymous|Synonymous,stop_gained|Stop Gained,frameshift|Frameshift,splice_donor|Splice Donor,splice_acceptor|Splice Acceptor,intron|Intron,3_prime_utr|3' UTR,5_prime_utr|5' UTR,non_coding|Non-coding,.|Intergenic,others|Other filterType.consequence multipleListOr filterLabel.consequence Consequence # Source database filter filterValues.sources AllOfUs|AllOfUs,SPARK|SPARK WES,SFARI_WGS|SFARI WGS,GenomeAsia|GenomeAsia SNVs,GenomeAsiaIndel|GenomeAsia Indels,KOVA|KOVA Korea,ToMMo|ToMMo Japan,IndiGen|IndiGenomes India,FinnGen|FinnGen Finland,Saudi|Saudi,SweGen|SweGen Sweden,TOPMed|TOPMed,ABraOM|ABraOM Brazil,ALFA|ALFA,MGRB|MGRB Australia,HRC|HRC,MexBB|Mexico Biobank,SGDP|SGDP,HGDP1kG|gnomAD HGDP+1kG,GREGoR|GREGoR,SCHEMA|SCHEMA,GA4K|GA4K PacBio LR,CoLoRSdb|CoLoRSdb PacBio LR,SVatalog|SVatalog 101 10XG SR,Tishkoff180|Tishkoff 180 African WGS,NPM|NPM Singapore filterType.sources multipleListOr filterLabel.sources Source Database # Length filters filterByRange.refLen on filterLabel.refLen Reference Length filterByRange.altLen on filterLabel.altLen Alternate Length filterByRange.varLen on filterLabel.varLen Length Change # Max AF filter filterByRange.maxAF on filterLabel.maxAF Max Allele Frequency filterLimits.maxAF 0:1 # Total AC filter filterByRange.totalAC on filterLabel.totalAC Total Allele Count (all databases) # Per-database AF filters filterByRange.AllOfUsAF on filterLabel.AllOfUsAF AllOfUs AF filterByRange.SPARKAF on filterLabel.SPARKAF SPARK WES AF filterByRange.SFARI_WGSAF on filterLabel.SFARI_WGSAF SFARI WGS AF filterByRange.GenomeAsiaAF on filterLabel.GenomeAsiaAF GenomeAsia SNVs AF filterByRange.GenomeAsiaIndelAF on filterLabel.GenomeAsiaIndelAF GenomeAsia Indels AF filterByRange.KOVAAF on filterLabel.KOVAAF KOVA Korea AF filterByRange.ToMMoAF on filterLabel.ToMMoAF ToMMo Japan AF filterByRange.IndiGenAF on filterLabel.IndiGenAF IndiGenomes India AF filterByRange.FinnGenAF on filterLabel.FinnGenAF FinnGen Finland AF filterByRange.SaudiAF on filterLabel.SaudiAF Saudi AF filterByRange.SweGenAF on filterLabel.SweGenAF SweGen Sweden AF filterByRange.TOPMedAF on filterLabel.TOPMedAF TOPMed AF filterByRange.ABraOMAF on filterLabel.ABraOMAF ABraOM Brazil AF filterByRange.ALFAAF on filterLabel.ALFAAF ALFA AF filterByRange.MGRBAF on filterLabel.MGRBAF MGRB Australia AF filterByRange.HRCAF on filterLabel.HRCAF HRC AF filterByRange.MexBBAF on filterLabel.MexBBAF Mexico Biobank AF filterByRange.SGDPAF on filterLabel.SGDPAF SGDP AF filterByRange.HGDP1kGAF on filterLabel.HGDP1kGAF gnomAD HGDP+1kG AF (4k cohort) filterByRange.GREGoRAF on filterLabel.GREGoRAF GREGoR AF filterByRange.SCHEMAAF on filterLabel.SCHEMAAF SCHEMA AF filterByRange.GA4KAF on filterLabel.GA4KAF GA4K PacBio LR AF filterByRange.CoLoRSdbAF on filterLabel.CoLoRSdbAF CoLoRSdb PacBio LR AF filterByRange.SVatalogAF on filterLabel.SVatalogAF SVatalog 101 10XG SR AF filterByRange.Tishkoff180AF on filterLabel.Tishkoff180AF Tishkoff 180 African WGS AF filterByRange.NPMAF on filterLabel.NPMAF NPM Singapore AF # Per-database AC filters filterByRange.AllOfUsAC on filterLabel.AllOfUsAC AllOfUs AC filterByRange.SPARKAC on filterLabel.SPARKAC SPARK WES AC filterByRange.SFARI_WGSAC on filterLabel.SFARI_WGSAC SFARI WGS AC filterByRange.GenomeAsiaAC on filterLabel.GenomeAsiaAC GenomeAsia SNVs AC filterByRange.GenomeAsiaIndelAC on filterLabel.GenomeAsiaIndelAC GenomeAsia Indels AC filterByRange.KOVAAC on filterLabel.KOVAAC KOVA Korea AC filterByRange.ToMMoAC on filterLabel.ToMMoAC ToMMo Japan AC filterByRange.IndiGenAC on filterLabel.IndiGenAC IndiGenomes India AC filterByRange.FinnGenAC on filterLabel.FinnGenAC FinnGen Finland AC filterByRange.SaudiAC on filterLabel.SaudiAC Saudi AC filterByRange.SweGenAC on filterLabel.SweGenAC SweGen Sweden AC filterByRange.TOPMedAC on filterLabel.TOPMedAC TOPMed AC filterByRange.ABraOMAC on filterLabel.ABraOMAC ABraOM Brazil AC filterByRange.ALFAAC on filterLabel.ALFAAC ALFA AC filterByRange.MGRBAC on filterLabel.MGRBAC MGRB Australia AC filterByRange.HRCAC on filterLabel.HRCAC HRC AC filterByRange.MexBBAC on filterLabel.MexBBAC Mexico Biobank AC filterByRange.SGDPAC on filterLabel.SGDPAC SGDP AC filterByRange.HGDP1kGAC on filterLabel.HGDP1kGAC gnomAD HGDP+1kG AC (4k cohort) filterByRange.GREGoRAC on filterLabel.GREGoRAC GREGoR AC filterByRange.SCHEMAAC on filterLabel.SCHEMAAC SCHEMA AC filterByRange.GA4KAC on filterLabel.GA4KAC GA4K PacBio LR AC filterByRange.CoLoRSdbAC on filterLabel.CoLoRSdbAC CoLoRSdb PacBio LR AC filterByRange.SVatalogAC on filterLabel.SVatalogAC SVatalog 101 10XG SR AC filterByRange.Tishkoff180AC on filterLabel.Tishkoff180AC Tishkoff 180 African WGS AC filterByRange.NPMAC on filterLabel.NPMAC NPM Singapore AC # Population-specific AF filters # AllOfUs local-ancestry populations # NB: these are local-ancestry-stratified frequencies (per-position, per-haplotype-class), # NOT the AllOfUs paper's global Rye ancestry categories. See varFreqs.html for details. filterByRange.AllOfUsAF_AFR on filterLabel.AllOfUsAF_AFR AllOfUs African AF (local ancestry) filterByRange.AllOfUsAF_AMR on filterLabel.AllOfUsAF_AMR AllOfUs Indigenous American AF (local ancestry) filterByRange.AllOfUsAF_EAS on filterLabel.AllOfUsAF_EAS AllOfUs East Asian AF (local ancestry) filterByRange.AllOfUsAF_EUR on filterLabel.AllOfUsAF_EUR AllOfUs European AF (local ancestry) filterByRange.AllOfUsAF_OCE on filterLabel.AllOfUsAF_OCE AllOfUs Oceanian AF (local ancestry) filterByRange.AllOfUsAF_SAS on filterLabel.AllOfUsAF_SAS AllOfUs South Asian AF (local ancestry) filterByRange.AllOfUsAC_AFR on filterLabel.AllOfUsAC_AFR AllOfUs African AC (local ancestry) filterByRange.AllOfUsAC_AMR on filterLabel.AllOfUsAC_AMR AllOfUs Indigenous American AC (local ancestry) filterByRange.AllOfUsAC_EAS on filterLabel.AllOfUsAC_EAS AllOfUs East Asian AC (local ancestry) filterByRange.AllOfUsAC_EUR on filterLabel.AllOfUsAC_EUR AllOfUs European AC (local ancestry) filterByRange.AllOfUsAC_OCE on filterLabel.AllOfUsAC_OCE AllOfUs Oceanian AC (local ancestry) filterByRange.AllOfUsAC_SAS on filterLabel.AllOfUsAC_SAS AllOfUs South Asian AC (local ancestry) # GenomeAsia SNVs populations (7 groups in source VCF) filterByRange.GenomeAsiaAF_NEA on filterLabel.GenomeAsiaAF_NEA GenomeAsia SNVs Northeast Asian AF filterByRange.GenomeAsiaAF_SEA on filterLabel.GenomeAsiaAF_SEA GenomeAsia SNVs Southeast Asian AF filterByRange.GenomeAsiaAF_SAS on filterLabel.GenomeAsiaAF_SAS GenomeAsia SNVs South Asian AF filterByRange.GenomeAsiaAF_OCE on filterLabel.GenomeAsiaAF_OCE GenomeAsia SNVs Oceanian AF filterByRange.GenomeAsiaAF_AMR on filterLabel.GenomeAsiaAF_AMR GenomeAsia SNVs American AF filterByRange.GenomeAsiaAF_AFR on filterLabel.GenomeAsiaAF_AFR GenomeAsia SNVs African AF filterByRange.GenomeAsiaAF_WER on filterLabel.GenomeAsiaAF_WER GenomeAsia SNVs Western European Ref AF filterByRange.GenomeAsiaAC_NEA on filterLabel.GenomeAsiaAC_NEA GenomeAsia SNVs Northeast Asian AC filterByRange.GenomeAsiaAC_SEA on filterLabel.GenomeAsiaAC_SEA GenomeAsia SNVs Southeast Asian AC filterByRange.GenomeAsiaAC_SAS on filterLabel.GenomeAsiaAC_SAS GenomeAsia SNVs South Asian AC filterByRange.GenomeAsiaAC_OCE on filterLabel.GenomeAsiaAC_OCE GenomeAsia SNVs Oceanian AC filterByRange.GenomeAsiaAC_AMR on filterLabel.GenomeAsiaAC_AMR GenomeAsia SNVs American AC filterByRange.GenomeAsiaAC_AFR on filterLabel.GenomeAsiaAC_AFR GenomeAsia SNVs African AC filterByRange.GenomeAsiaAC_WER on filterLabel.GenomeAsiaAC_WER GenomeAsia SNVs Western European Ref AC # gnomAD HGDP+1kG: per-population AF/AC values are from the FULL gnomAD v3.1.2 # release (~76k genomes), not the 4,094-genome HGDP+1kG cohort. Only the # cohort-level HGDP1kGAF / HGDP1kGAC fields above reflect the 4k-cohort. filterByRange.HGDP1kGAF_afr on filterLabel.HGDP1kGAF_afr gnomAD v3.1.2 African AF (full release) filterByRange.HGDP1kGAF_ami on filterLabel.HGDP1kGAF_ami gnomAD v3.1.2 Amish AF (full release) filterByRange.HGDP1kGAF_amr on filterLabel.HGDP1kGAF_amr gnomAD v3.1.2 Latino AF (full release) filterByRange.HGDP1kGAF_asj on filterLabel.HGDP1kGAF_asj gnomAD v3.1.2 Ashkenazi Jewish AF (full release) filterByRange.HGDP1kGAF_eas on filterLabel.HGDP1kGAF_eas gnomAD v3.1.2 East Asian AF (full release) filterByRange.HGDP1kGAF_fin on filterLabel.HGDP1kGAF_fin gnomAD v3.1.2 Finnish AF (full release) filterByRange.HGDP1kGAF_mid on filterLabel.HGDP1kGAF_mid gnomAD v3.1.2 Middle Eastern AF (full release) filterByRange.HGDP1kGAF_nfe on filterLabel.HGDP1kGAF_nfe gnomAD v3.1.2 Non-Finnish European AF (full release) filterByRange.HGDP1kGAF_oth on filterLabel.HGDP1kGAF_oth gnomAD v3.1.2 Other AF (full release) filterByRange.HGDP1kGAF_sas on filterLabel.HGDP1kGAF_sas gnomAD v3.1.2 South Asian AF (full release) filterByRange.HGDP1kGAC_afr on filterLabel.HGDP1kGAC_afr gnomAD v3.1.2 African AC (full release) filterByRange.HGDP1kGAC_ami on filterLabel.HGDP1kGAC_ami gnomAD v3.1.2 Amish AC (full release) filterByRange.HGDP1kGAC_amr on filterLabel.HGDP1kGAC_amr gnomAD v3.1.2 Latino AC (full release) filterByRange.HGDP1kGAC_asj on filterLabel.HGDP1kGAC_asj gnomAD v3.1.2 Ashkenazi Jewish AC (full release) filterByRange.HGDP1kGAC_eas on filterLabel.HGDP1kGAC_eas gnomAD v3.1.2 East Asian AC (full release) filterByRange.HGDP1kGAC_fin on filterLabel.HGDP1kGAC_fin gnomAD v3.1.2 Finnish AC (full release) filterByRange.HGDP1kGAC_mid on filterLabel.HGDP1kGAC_mid gnomAD v3.1.2 Middle Eastern AC (full release) filterByRange.HGDP1kGAC_nfe on filterLabel.HGDP1kGAC_nfe gnomAD v3.1.2 Non-Finnish European AC (full release) filterByRange.HGDP1kGAC_oth on filterLabel.HGDP1kGAC_oth gnomAD v3.1.2 Other AC (full release) filterByRange.HGDP1kGAC_sas on filterLabel.HGDP1kGAC_sas gnomAD v3.1.2 South Asian AC (full release) # GREGoR populations filterByRange.GREGoRAF_AFF on filterLabel.GREGoRAF_AFF GREGoR Affected AF filterByRange.GREGoRAF_UNA on filterLabel.GREGoRAF_UNA GREGoR Unaffected AF filterByRange.GREGoRAF_UNK on filterLabel.GREGoRAF_UNK GREGoR Unknown AF filterByRange.GREGoRAC_AFF on filterLabel.GREGoRAC_AFF GREGoR Affected AC filterByRange.GREGoRAC_UNA on filterLabel.GREGoRAC_UNA GREGoR Unaffected AC filterByRange.GREGoRAC_UNK on filterLabel.GREGoRAC_UNK GREGoR Unknown AC # NPM Singapore ancestry groups filterByRange.NPMAF_Chinese on filterLabel.NPMAF_Chinese NPM Singapore Chinese AF filterByRange.NPMAF_Malay on filterLabel.NPMAF_Malay NPM Singapore Malay AF filterByRange.NPMAF_Indian on filterLabel.NPMAF_Indian NPM Singapore Indian AF filterByRange.NPMAC_Chinese on filterLabel.NPMAC_Chinese NPM Singapore Chinese AC filterByRange.NPMAC_Malay on filterLabel.NPMAC_Malay NPM Singapore Malay AC filterByRange.NPMAC_Indian on filterLabel.NPMAC_Indian NPM Singapore Indian AC skipEmptyFields on track allofus shortLabel AllOfUs v7 245k WGS longLabel Variant Frequencies: AllOfUs v7 - 245k WGS, local-ancestry-stratified, AC>=20 type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_allofus/allOfUs.locAncFreq.vcf.gz dataVersion V7 visibility dense tableBrowser off priority 0.5 #track me #shortLabel Regeneron Million Exomes 983k WES #longLabel Variant Frequencies: Regeneron One Million Exomes (ME) Project - 983k WGS #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/me/me.freq.vcf.gz #visibility pack #type vcfTabix #hapClusterEnabled true #dataVersion 10/04/2023, v1.1.3 #tableBrowser off #priority 1 track topmed shortLabel NHLBI TOPMed 10 151k WGS longLabel Variant Frequencies: NHLBI TOPMed - 151k WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_topmed/topmed10.vcf.gz dataVersion Freeze 10 visibility dense tableBrowser off priority 2 track sfariSparkExomes shortLabel SFARI SPARK 140k WES longLabel Variant Frequencies: SFARI SPARK - 140k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/SPARK.iWES_v3.2024_08.deepvariant.norm.vcf.gz dataVersion iWES v3 2024_08 visibility dense tableBrowser off priority 2.5 track sfariSparkWgs shortLabel SFARI SPARK 12k WGS longLabel Variant Frequencies: SFARI SPARK - 12,519 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_sfari/wgs_12519_genome.deepvariant.norm.vcf.gz dataVersion iWGS v1.1 visibility dense priority 2.5 html sfariSparkExomes tableBrowser off #track mcps #shortLabel Mexico City Prospective Study 10k WGS+141k WES #longLabel Variant Frequencies: Mexico City Prospective Study (MCPS) #tableBrowser off #parent varFreqs on #bigDataUrl /gbdb/$D/varFreqs/mcps/mcps.freq.vcf.gz #visibility pack #type vcfTabix #dataVersion May 2023 (v1.2.0) #priority 3 track tommo60kjpn shortLabel Japan ToMMo 61k WGS longLabel Variant Frequencies: Japan 61k - ToMMo SNV+Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz visibility dense dataVersion 2025-06-16 priority 5 track wbbc shortLabel China WBBC 4.5k WGS longLabel Variant Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/wbbc/wbbc.vcf.gz visibility dense dataVersion Phase I v20210103 priority 5.5 + track chinamap + shortLabel China ChinaMAP 10.5k WGS + longLabel Variant Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population + type vcfTabix + parent varFreqs on + bigDataUrl /gbdb/$D/varFreqs/_chinamap/chinamap.vcf.gz + visibility dense + dataVersion Phase 1 (v2020-03.beta) + priority 5.55 + tableBrowser off + track tpmi shortLabel Taiwan TPMI Axiom array longLabel Variant Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tpmi/tpmi.vcf.gz visibility dense dataVersion Axiom TPM1 2022-06 priority 5.6 tableBrowser off track alfaVcf shortLabel NCBI ALFA 408k mixed longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/alfa/ALFA.vcf.gz visibility dense dataVersion R4 priority 4.1 url https://www.ncbi.nlm.nih.gov/snp/$$#frequency_tab urlLabel NCBI Variation Page track finngen parent varFreqs on visibility dense type vcfTabix shortLabel FinnGen R12 500k imputed longLabel Variant Frequencies: Finland FinnGen - 500k samples, arrays, imputation used 8.5k WGS priority 4.5 bigDataUrl /gbdb/$D/varFreqs/_finngen/finnge_R12_annotated_variants_v1.vcf.gz dataVersion R12 tableBrowser off track ukbb parent varFreqs on visibility dense type vcfTabix shortLabel UK Biobank 361k imputed longLabel Variant Frequencies: UK Biobank Genotypes - 361k White British, Neale Lab Round 2 imputed priority 4.6 bigDataUrl /gbdb/$D/varFreqs/ukbb/ukbb.vcf.gz dataVersion Neale Lab R2 08-2018 track swefreq parent varFreqs on visibility dense type vcfTabix shortLabel Sweden SweGen 1k WGS longLabel Variant Frequencies: Sweden SweGen - 1k WGS priority 4.7 bigDataUrl /gbdb/$D/varFreqs/_swefreq/swegen_frequencies_fixploidy_GRCh38_20190204.vcf.gz dataVersion 20251201 tableBrowser off track mgrb shortLabel Australia MGRB 4k WGS longLabel Variant Frequencies: Australia Medical Genome Reference Bank - 4,011 WGS type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mgrb/MGRB.phase3.GRCh38.norm.vcf.gz dataVersion Phase 3 visibility dense # no downloads as per Matt Hobbs email Jan 28 2026 tableBrowser off track gasp shortLabel GenomeAsia 1.7k SNVs longLabel Variant Frequencies: GenomeAsia Pilot - Substitutions type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.subst.vcf.gz visibility dense dataVersion Pilot 2019 (lifted to hg38, May 2026) track gaspIndel shortLabel GenomeAsia 1.7k Indels longLabel Variant Frequencies: GenomeAsia Pilot - Indels type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga100k/ga100k.indels.vcf.gz visibility dense dataVersion Pilot 2019 (lifted to hg38, May 2026) html gasp track abraom shortLabel Brazil ABraOM 1k WGS longLabel Variant Frequencies: ABraOM Brazil - 1,171 unrelated individuals type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/abraom/abraom.vcf.gz visibility dense dataVersion SABE-WGS-1171 Sep 2020 track indigenomes shortLabel India IndiGenomes 1k WGS longLabel Variant Frequencies: IndiGenomes India - 1,029 samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/indigenomes/IndiGenomes_Variants.vcf.gz visibility dense dataVersion IndiGen pilot (Jain 2021) track kova shortLabel Korea KOVA 5.3k mixed longLabel Variant Frequencies: KOVA Korea - 5305 samples, 1.9k WGS+3.4k WES type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_kova/kova.v7.vcf.gz visibility dense tableBrowser off dataVersion V7 track npm shortLabel Singapore NPM 9.7k WGS longLabel Variant Frequencies: NPM Singapore - 9,770 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_npm/SG10K_Health_r5.3.2.sites.vcf.bgz visibility dense tableBrowser off dataVersion r5.3.2 track hrc shortLabel HRC 30k WGS longLabel Variant Frequencies: Haplotype Reference Consortium - 30k WGS (excl. 1000 Genomes) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hrc/hrc.vcf.gz visibility dense dataVersion r1.1 track saudi shortLabel Saudi Genome 302 WGS longLabel Variant Frequencies: Saudi Genome Project - 302 WGS samples type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/saudi/saudi.vcf.gz visibility dense dataVersion SHGP (figshare 51297884, 2025) track schema shortLabel SCHEMA 121k WES Sz longLabel Variant Frequencies: SCHEMA Schizophrenia Exome Meta-Analysis - WES 24k cases, 97k controls type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/schema/SCHEMA_variant_results_withAF.vcf.gz visibility dense dataVersion 2022 priority 4.9 url https://schema.broadinstitute.org/ urlLabel SCHEMA Browser track mxbFreq shortLabel Mexico Biobank 6k Array longLabel Variant Frequencies: Mexico Biobank - 6,011 individuals, genotyping array type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_mxb/mxb.freq.vcf.gz visibility dense dataVersion Nov 2025 (hg38 lift) tableBrowser off priority 6 track sgdpFreq shortLabel SGDP 279 WGS longLabel Variant Frequencies: Simons Genome Diversity Project - 279 WGS, 142 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/sgdpFreq/sgdp.freq.vcf.gz visibility dense dataVersion 2016-12-07 (hg38 lift) priority 7 track gregor shortLabel GREGoR R4 3.6k WGS longLabel Variant Frequencies: GREGoR Consortium - Release 4, 3,624 WGS samples, rare disease families type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/gregor/gregor.vcf.gz visibility dense dataVersion R04 (Oct 2025) priority 8 track hgdp1kFreq shortLabel gnomAD HGDP+1kG 4k WGS longLabel Variant Frequencies: gnomAD HGDP + 1000 Genomes - 4,094 WGS, 80 populations type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/hgdp1kFreq/hgdp1k.freq.vcf.gz visibility dense dataVersion gnomAD v3.1.2 priority 8 track ga4kSnv shortLabel GA4K 552 PacBio LR longLabel Variant Frequencies: GA4K Children's Mercy - 552 PacBio HiFi WGS, pediatric RD type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/ga4k/ga4kSnv.vcf.gz visibility dense dataVersion Cohen 2022 release priority 9 track colorsDbSnv shortLabel CoLoRSdb 1k LR SNV/Ind longLabel Variant Frequencies: CoLoRSdb v1.2.0 - 1,027 PacBio HiFi WGS, SNV/indel callset type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/colorsDb/colorsDbSnv.vcf.gz visibility dense dataVersion v1.2.0 priority 9.5 track svatalogSnv shortLabel SVatalog 101 WGS longLabel Variant Frequencies: GWAS SVatalog - 101 samples, 10X Genomics linked-read SNPs type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/svatalog/svatalog.vcf.gz visibility dense dataVersion Chirmade 2025 release priority 10 track tishkoff180 shortLabel 12 Afr Pops 180 WGS longLabel Variant Frequencies: 180 WGS from 12 Indigenous African Populations (Fan 2023) type vcfTabix parent varFreqs on bigDataUrl /gbdb/$D/varFreqs/_tishkoff/tishkoff180.vcf.gz visibility dense dataVersion Cell 2023 (hg19 lift) tableBrowser off priority 7.5