22fc293ddc00fce956d75fbcdb237e5d19d08fd5 max Thu Sep 3 14:39:29 2026 -0700 Three more Imprinting subtracks on hg38: Geneimprint, Akbari iDMRs, OMIM Geneimprint: the human catalog of imprinted and candidate imprinted genes from geneimprint.com, 274 genes. The catalog gives only a cytogenetic band, so symbols are resolved against the HGNC track, with fallbacks for small RNA clusters and for symbols HGNC has retired. Akbari iDMRs: the 192 imprinted differentially methylated regions that Akbari et al. 2023 (PMID 36777186) compiled from five genome-wide studies. Their published coordinates are 1-based inclusive, not bed, as their own PatMat reader shows, so the starts are shifted. OMIM: the 459 loci that OMIM curates as imprinted. That call is published only through GeneScout and is in no OMIM download file, so the input is a GeneScout export made by hand from a browser. OMIM phenotype entries, which are mapped disease regions up to 90 Mb rather than gene positions, are left out. Also unifies the color scheme across the collection, so vermillion always means the maternal copy, blue the paternal copy and gray no parent of origin, and relates the collection to the Human Methylation Atlas. refs #37599 diff --git src/hg/makeDb/trackDb/relatedTracks.ra src/hg/makeDb/trackDb/relatedTracks.ra index 0a242190bbd..92c6141e216 100644 --- src/hg/makeDb/trackDb/relatedTracks.ra +++ src/hg/makeDb/trackDb/relatedTracks.ra @@ -12,30 +12,33 @@ # "Short Label: reason", so do not begin the reason with the track's own name. # 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 gnomadVariants View associated variants hg38 gnomadVariants 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 >imprinting humanMethylationAtlasSummary Methylation of purified cell types, from the Kaplan lab +hg38 >humanMethylationAtlasSummary imprinting Imprinted genes and allele-specific methylation + hg38 gnomadStr strVar Population-level short tandem repeat and VNTR variation from multiple projects hg38 strVar gnomadStr Short tandem repeat genotypes at disease-associated loci, from gnomAD v3.1.3 hg38 varFreqs gnomadVariants Harmonized allele frequencies from ~800,000 exomes and genomes hg38 gnomadVariants varFreqs Allele frequencies from population-scale projects worldwide, not reprocessed by gnomAD hg38 varFreqs strVar Population-level short tandem repeat and VNTR variation from multiple projects hg38 strVar varFreqs SNV and indel allele frequencies from population-scale sequencing and array projects hg38 >revel liftHg19 REVEL is based on hg19 and lifted to hg38 with these liftOver chain alignments hg38 revel caddSuper A similar deleteriousness score, not used as an input by REVEL hg38 caddSuper revel A similar deleteriousness score hg38 liftHg19 grcIncidentDb Reasons why the assembly was changed in this region