ce180274fa3ba3db5c10ecbd9ae2479d4816e972
max
  Tue Mar 10 04:00:45 2026 -0700
Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies

Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of
hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05,
grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR.
Track added to existing MPRAs superTrack, refs #34284

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

diff --git src/hg/makeDb/scripts/mpravardb/mpravardb.as src/hg/makeDb/scripts/mpravardb/mpravardb.as
new file mode 100644
index 00000000000..927c655c1b9
--- /dev/null
+++ src/hg/makeDb/scripts/mpravardb/mpravardb.as
@@ -0,0 +1,26 @@
+table mpravardb
+"MPRA Variant Database - experimentally tested regulatory variants from MPRA studies"
+    (
+    string chrom;        "Reference sequence chromosome or scaffold"
+    uint chromStart;     "Start position in chromosome"
+    uint chromEnd;       "End position in chromosome"
+    string name;         "Variant name (rsID or chr:pos:ref>alt)"
+    uint score;          "Score from 0-1000 based on -log10(pvalue)"
+    char[1] strand;      "Strand (always .)"
+    uint thickStart;     "Same as chromStart"
+    uint thickEnd;       "Same as chromEnd"
+    uint reserved;       "itemRgb - color by significance"
+    string ref;          "Reference allele"
+    string alt;          "Alternate allele"
+    string rsid;         "dbSNP rsID"
+    string disease;      "Associated disease or trait"
+    string cellLine;     "Cell line used in MPRA experiment"
+    string description;  "Description of the MPRA experiment"
+    float log2FC;        "Log2 fold change (alt vs ref allele activity)"
+    float pvalue;        "P-value for allelic difference"
+    float fdr;           "False discovery rate"
+    string mpraStudy;    "MPRA study citation"
+    string _mouseOverLog2FC;  "log2FC rounded to 3 digits for mouseOver"
+    string _mouseOverPvalue;  "p-value rounded to 3 digits for mouseOver"
+    string _mouseOverFdr;     "FDR rounded to 3 digits for mouseOver"
+    )