f43f1239645183b88a00b3de83f74fd5553e6ce1 max Thu Mar 12 07:52:35 2026 -0700 Add gnomAD STR genotype track under gnomadVariants supertrack 87 disease-associated STR loci from gnomAD v3.1.3, aggregated from ~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5). Includes allele frequency distributions and population breakdowns. Added relatedTracks links to strVar supertrack, refs #35420, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index a24365e7893..11190ea044b 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -2,30 +2,33 @@ # ucscDb track trackLinkingTo reason # hg38: hg38 knownGene knownGeneArchive View previous versions of GENCODE Genes hg38 knownGeneArchive knownGene View the latest GENCODE Genes version hg38 miRnaAtlas nonCodingRNAs View associated precursor miRnas hg38 nonCodingRNAs miRnaAtlas View expression of cleaved miRnas hg38 caddSuper gnomad View associated variants hg38 gnomad caddSuper View CADD scores for this variant and region hg38 constraintSuper gnomadPLI Predicted constraint metrics from gnomAD hg38 gnomadPLI constraintSuper Container track of various constraint scores +hg38 gnomadStr strVar gnomAD STR genotypes at disease-associated loci; STR Variation supertrack has population-level STR data +hg38 strVar gnomadStr Population-level STR variation; gnomAD STR track has disease-associated locus genotypes + hg38 revel liftHg38 Revel is based on hg19 and lifted to hg38. liftOver "chain" alignment from hg19 to hg38 hg38 liftHg38 revel Revel scores were lifted using UCSC liftOver chains from hg38 hg38 revel caddSuper CADD, a similar deleteriousness score, and not used as an input by REVEL hg38 caddSuper revel REVEL, a similar deleteriousness score hg38 liftHg19 grcIncidentDb GRC Incident database, to explore reasons why the assembly was changed hg38 grcIncidentDb liftHg19 LiftOver for hg38, explores how incident regions aligned between human assemblies hg38 ReMap liftHg19 NCBI ReMap, even though it has the same name, is a liftOver-like hg19/hg38 alignment, and unrelated to the ReMap database hg38 liftHg19 ReMap ReMap, even though it has the same name, is a database of transcription factor binding sites, unrelated to NCBI ReMap hg38 ReMap jaspar JASPAR is a database of predicted TF binding sites, based on short DNA matches. Unlike ReMap, the data is purely computational. hg38 jaspar ReMap ReMap is a database of TF binding sites inferred from ChIP-Seq Data. Unlike JASPAR predictions, these sites are supported by functional assay