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/scripts/imprinting/geneimprint.as src/hg/makeDb/scripts/imprinting/geneimprint.as
new file mode 100644
index 00000000000..381f67174f3
--- /dev/null
+++ src/hg/makeDb/scripts/imprinting/geneimprint.as
@@ -0,0 +1,22 @@
+table geneimprint
+"Geneimprint catalog of imprinted and candidate imprinted genes, symbols resolved to hg38 coordinates"
+    (
+    string chrom;              "Chromosome (or contig, scaffold, etc.)"
+    uint   chromStart;         "Start position in chromosome"
+    uint   chromEnd;           "End position in chromosome"
+    string name;               "Gene name in the Geneimprint catalog"
+    uint   score;              "Score (unused, always 0)"
+    char[1] strand;            "+ or - for strand"
+    uint   thickStart;         "Start of thick display"
+    uint   thickEnd;           "End of thick display"
+    uint   reserved;           "Color, set from the expressed allele"
+    string status;             "Imprint Status|Evidence level assigned by Geneimprint"
+    string expressedAllele;    "Expressed Allele|Parental copy that is expressed"
+    lstring aliases;           "Aliases|Other names for this gene, as listed by Geneimprint"
+    string catalogBand;        "Catalog Band|Cytogenetic band as given by Geneimprint"
+    string hgncSymbol;         "Resolved Symbol|Approved symbol of the locus the coordinates come from"
+    string hgncId;             "HGNC ID|Identifier of the resolved locus, empty if resolved through RefSeq"
+    lstring geneName;          "Gene Description|Full name of the resolved locus"
+    string locusType;          "Locus Type|Kind of locus, e.g. protein coding or small nucleolar RNA"
+    string resolvedBy;         "Resolved By|Which name matched: current symbol, previous symbol, alias, small RNA cluster or RefSeq"
+    )