MPRAu pooled CMS+GWAS 3′UTR variant screen in SK-N-SH
Genome-wide functional screen of 3′UTR variants uncovers causal variants for human disease and evolutionThe pooled CMS+GWAS 100-bp reference/alternate 3′UTR library was assayed in SK-N-SH neuroblastoma cells using an episomal GFP reporter with a random hexamer barcode; steady-state RNA output was compared with plasmid DNA input across four transfections.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
Basal / Untreated
Episomal plasmid MPRAu: 100-bp human 3′UTR oligos centered on a reference/alternate variant were cloned downstream of GFP and adjacent to a random hexamer barcode. CMS+GWAS pooled library; reporter RNA was collected 48 hours after transfection and compared with plasmid DNA input using DESeq2.
Processed data
50 rows per page. Click a cell to inspect its full value.
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 49 definitions
- mpra_variant_id
- Unique MPRAu reference/alternate pair identifier, preserving the tested sequence background.
- variant_id
- Variant identifier independent of alternate sequence-background contexts.
- variant_class
- Source category: GWAS-linked, Rare GTEx, or CMS/selection or random control.
- library_source
- Array source used for the HEK293FT counts, or the pooled CMS+GWAS library used in the other cell types.
- allelic_background
- Reference background, alternate allelic background, or additional sequence context encoded by the source ID.
- chromosome
- hg19 chromosome.
- variant_start_hg19
- 1-based hg19 start coordinate of the tested variant; filled from the source or an unambiguous coordinate-style variant ID.
- variant_end_hg19
- 1-based hg19 end coordinate of the tested variant; blank when unresolved.
- ref_allele
- Reference allele used in the pair.
- alt_allele
- Alternate allele used in the pair.
- strand
- Source oligo strand.
- gene_symbols
- Comma-separated gene symbols annotated for the oligo.
- gene_ids
- Comma-separated Ensembl gene identifiers annotated for the oligo.
- transcripts
- Comma-separated Gencode transcript identifiers annotated for the oligo.
- oligo_starts_hg19
- Source hg19 oligo start coordinate(s), including comma-separated exon segments when applicable.
- oligo_ends_hg19
- Source hg19 oligo end coordinate(s), including comma-separated exon segments when applicable.
- other_variants_in_oligo_window
- Other variants or source indexing flags in the tested oligo window.
- ref_oligo_id
- Oligonucleotide construct identifier for the reference allele.
- alt_oligo_id
- Oligonucleotide construct identifier for the alternate allele.
- gwas_tag_snps
- GWAS Catalog tag SNPs linked to the tested variant.
- gwas_traits
- GWAS Catalog traits associated with the linked tag SNPs.
- gwas_pmids
- PubMed IDs for linked GWAS reports.
- gwas_ld
- Reported LD values for the tested variant/tag-SNP links.
- gwas_pvalue_minus_log10
- Reported -log10 GWAS p-values for linked tag SNPs.
- gwas_odds_ratio
- Reported odds ratios or effect estimates for linked tag SNPs.
- gwas_risk_alleles
- Reported risk alleles for linked tag SNPs.
- rare_gene_id
- Ensembl gene identifier for rare-variant annotation.
- rare_median_z
- Median expression outlier Z-score for the rare-variant annotation.
- rare_outlier_class
- Rare-variant expression-outlier/control class.
- rare_river_score
- RIVER rare-variant functionality score.
- ref_mean_plasmid_count
- Mean raw plasmid DNA count across applicable source replicates for the reference oligo.
- alt_mean_plasmid_count
- Mean raw plasmid DNA count across applicable source replicates for the alternate oligo.
- mean_plasmid_count
- Mean of the reference and alternate oligo plasmid counts used for package QC.
- ref_mean_rna_count
- Mean raw reporter RNA count across applicable source replicates for the reference oligo.
- alt_mean_rna_count
- Mean raw reporter RNA count across applicable source replicates for the alternate oligo.
- ref_activity_log2fc
- Published DESeq2 log2 fold-change for reference reporter RNA versus plasmid DNA.
- ref_activity_lfcse
- Published DESeq2 standard error for reference activity.
- ref_activity_pvalue
- Published DESeq2 p-value for reference activity.
- ref_activity_padj
- Published BH-adjusted p-value for reference activity.
- alt_activity_log2fc
- Published DESeq2 log2 fold-change for alternate reporter RNA versus plasmid DNA.
- alt_activity_lfcse
- Published DESeq2 standard error for alternate activity.
- alt_activity_pvalue
- Published DESeq2 p-value for alternate activity.
- alt_activity_padj
- Published BH-adjusted p-value for alternate activity.
- allelic_skew_log2fc
- Published DESeq2 log2 fold-change for the alternate-versus-reference allelic skew.
- allelic_skew_lfcse
- Published DESeq2 standard error for the allelic skew.
- allelic_skew_pvalue
- Published DESeq2 p-value for the allelic skew.
- allelic_skew_padj
- Published BH-adjusted p-value for the allelic skew.
- tamvar
- TRUE when the source allelic-skew BH-adjusted p-value is <0.1 in this cell type.
- qc_pass
- TRUE for rows retained after paired-allele plasmid-count and complete-statistic QC.
Quality control
The authors filtered barcode-flanking sequences and retained oligos with a BWA alignment score ≥0.95; they report roughly 70–330 unique hexamer barcodes per oligo per replicate and applied DESeq2 with median-of-ratios normalization. For this package, both allele constructs were required to have mean plasmid counts ≥20 across the applicable source replicates, and the target-cell skew log2FC, standard error, p-value, BH-adjusted p-value, and both allele activity estimates had to be present. 13912 of 15,266 MPRAu pair rows passed this filter.
Curation notes
The study transfected CMS and GWAS arrays separately in HEK293FT and used a pooled CMS+GWAS library in the other cell types. mpra_variant_id preserves the source-defined allelic sequence background; IDs ending in _2 are alternate-background tests. Some alternate-background records omit oligo genomic coordinates in the source workbook; when possible, variant positions were backfilled from the matching base variant or coordinate-style variant ID. The processed table has one row per reference/alternate comparison and includes mean raw counts for QC context.