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 diff --git src/hg/makeDb/trackDb/human/hg38/mpra.html src/hg/makeDb/trackDb/human/hg38/mpra.html new file mode 100644 index 00000000000..3ad2ec75763 --- /dev/null +++ src/hg/makeDb/trackDb/human/hg38/mpra.html @@ -0,0 +1,209 @@ +

Description

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+The MPRAs super track contains tracks with results from +Massively Parallel Reporter Assays (MPRA), high-throughput experimental methods +that test thousands of genetic variants for their effects on gene regulation. +

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MPRAVarDB

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+The MPRAVarDB track shows 242,818 variants from 18 MPRA studies compiled +in the MPRAVarDB database +(Wang et al., 2024). +Each variant was experimentally tested in an MPRA experiment to evaluate whether it +affects transcriptional regulatory activity. The database covers over 30 cell lines +and 30 human diseases and traits, including neurodegenerative diseases, immune +disorders, melanoma, multiple myeloma, and autoimmune diseases. +

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Display Conventions

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+Items are colored by statistical significance: +

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+Each item shows the variant name (rsID when available, otherwise chr:pos:ref>alt), +the reference and alternate alleles, the associated disease or trait, cell line, +log2 fold change, p-value, and FDR. +

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Studies

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+The following table lists the 18 MPRA studies included in MPRAVarDB, with the number of +tested variants, diseases/traits, cell lines, and a brief description of the variant selection. +

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StudyVariantsDisease/TraitCell Line(s)Description
Griesemer et al., 202172,588NHGRI-EBI GWAS catalogGM12878, HEK293FT, HMEC, HepG2, K562, SKNSH3'UTR SNPs and indels in LD with GWAS catalog variants, variants under positive selection, and rare outlier expression variants from GTEx
Kircher et al., 201944,647Various (18 diseases including diabetes, cancer, blood disorders, limb malformations)HEK293T, HEL92.1.7, HaCaT, HeLa, HepG2, K562, LNCaP, MIN6, NIH/3T3, Neuro-2a, SK-MEL-28, SF7996Saturation mutagenesis of 20 disease-associated regulatory elements at single base-pair resolution
Abell et al., 202229,582eQTL (no specific disease)GM1287830,893 variants in LD with independent, common, top-ranked eQTL across 744 eGenes in the CEU cohort
Tewhey et al., 201627,138eQTL (no specific disease)GM1287832,373 variants associated with eQTLs in lymphoblastoid cell lines
Schuster et al., 202326,546Prostate cancerPC314,497 single-nucleotide mutations enriched in oncogenic pathways and 3'UTR regulatory elements
Mouri et al., 202214,551Autoimmune diseases (Crohn's, IBD, psoriasis, MS, RA, T1D, ulcerative colitis)JurkatGWAS variants from autoimmune disease loci tested for regulatory element activity in T cells
McAfee et al., 202310,310SchizophreniaHEK293s, HNPS5,173 fine-mapped schizophrenia GWAS variants
Cooper et al., 20225,340Alzheimer's disease, Progressive supranuclear palsyHEK293T5,706 noncoding SNVs from 25 AD and 9 PSP genome-wide significant loci
Long et al., 20223,980MelanomaC283T, UACC9031,992 risk-associated variants in tight LD (r2>0.8) from 54 melanoma risk loci
Myint et al., 20202,158Schizophrenia, Alzheimer's diseaseK562, SH-SY5Y1,049 SZ and 30 AD variants in 64 SZ loci and 9 AD loci
Choi et al., 20201,664MelanomaHEK293FT, UACC903GWAS melanoma risk variants
Ajore et al., 20221,582Multiple myelomaL363, MOLP81,039 variants in high LD (r2>0.8) at 23 MM risk loci
Klein et al., 20191,119OsteoarthritisSaos-21,605 SNPs in high LD (r2>0.8) at 35 lead SNPs associated with OA via GWAS
Lu et al., 20211,038Systemic lupus erythematosusGM12878, Jurkat18,312 variants in tight LD (r2>0.8) with 578 GWAS index variants at 531 loci
Mulvey & Dougherty, 2021275Major depressive disorderN2AOver 1,000 SNPs from 39 neuropsychiatric GWAS loci, selected by overlap with eQTL and histone marks
Ferraro et al., 2020150Rare variant expression (no specific disease)GM12878Rare variants contributing to extreme expression, allelic expression, and splicing across 49 GTEx tissues
Rao et al., 202188Alcohol use disorderBLA, CE, NAC, SFCSNPs in 3'UTR of 88 genes from allele-specific expression analysis (30 AUD subjects vs 30 controls)
Ulirsch et al., 201662Red blood cell traitsK562, K562+GATA12,756 variants in strong LD with 75 sentinel variants associated with RBC traits
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Methods

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+Data was downloaded from the +MPRAVarDB web server. +Variants originally mapped to hg19 (213,689 of 242,818) were lifted to hg38 +using liftOver. 114 variants could not be mapped and were excluded. +The remaining variants were merged with the 29,129 natively hg38-mapped variants +to produce a total of 239,028 hg38 records. +

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Data Access

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+The raw data can be explored interactively with the +Table Browser or the +Data Integrator. +The data can also be accessed from the command line using +bigBedToBed. +

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Credits

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+Thanks to Tao Wang and colleagues at the University of Florida for creating and +maintaining the MPRAVarDB database. +

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References

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+Wang T, Matreyek KA, Yang X. + +MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants using MPRA data. +Bioinformatics. 2024 Apr 15;40(4):btae201. +PMID: 38617248; +PMC: PMC11014600 +