CHD-risk variant enhancer MPRA in cardiac transcription-factor-expressing Flp-In 293 cells
Global Evaluation of Congenital Heart Disease-Associated Non-Coding VariantsA plasmid-based MPRA tested 5,431 CHD-associated variants expanded by linkage disequilibrium, represented by 14,524 allele sequences, in a Flp-In 293 reporter background expressing NKX2-5, GATA4, and TBX5. The packaged table contains allele-level activity, allelic fold change, source count/activity values, sequence context, and MPRA-derived cardiac regulatory annotations for the analyzed result set.
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; stable cardiac transcription-factor expression (NKX2-5, GATA4, and TBX5)
The authors cloned 170-bp hg38 allele-centered sequences, with 15-bp fixed adapters and degenerate 20-mer barcodes, upstream of an eGFP reporter under a minimal promoter in a pGL4.23-derived plasmid. Flp-In 293 cells were used for transfection; the base line already expressed NKX2-5 and GATA4 and was modified to express TBX5 by site-specific recombination. GFP transcripts were captured and sequenced, and normalized RNA:plasmid barcode ratios were used as CRE activity. The methods state five total transfections, while the supplied MPRA count/activity workbook exposes three analyzed biological replicates (r1-r3), which are retained in the table.
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 · 44 definitions
- element_id
- Unique oligo identifier from the MPRA counts sheet; the source uses Non-Ref in alternate-allele IDs.
- variant_id
- Variant rsID associated with the tested oligo.
- chromosome
- Chromosome label for the MPRA insert, standardized with a chr prefix.
- element_start_hg38
- Start coordinate of the MPRA insert from the supplied result sheet.
- element_end_hg38
- End coordinate of the MPRA insert from the supplied result sheet; element length is end minus start.
- variant_position_hg38
- Derived center coordinate, calculated as element_start_hg38 + 85 from the reported 84-bp upstream/85-bp downstream SNP design.
- element_length_bp
- Length of the genomic MPRA element calculated as element_end_hg38 - element_start_hg38.
- allele_class
- Canonical allele class: reference, alternate, or alternate_permuted_N for additional non-reference permutations.
- allele_label
- Allele label as reported in the MPRA fold-change workbook, such as Ref, Alt, Alt-1, or Alt-2.
- allele
- Nucleotide or indel allele inserted at the variant position.
- twist_oligo_sequence
- Full synthesized Twist oligo sequence for the element, including the 15-bp fixed adapters flanking the genomic insert.
- sequence_length_bp
- Length of the supplied synthesized oligo sequence in base pairs; indel constructs can be shorter than 200 bp.
- plasmid_barcode_count_r1
- Plasmid-library barcode count for analyzed biological replicate 1, from source column Plasmid_r1.
- plasmid_barcode_count_r2
- Plasmid-library barcode count for analyzed biological replicate 2, from source column Plasmid_r2.
- plasmid_barcode_count_r3
- Plasmid-library barcode count for analyzed biological replicate 3, from source column Plasmid_r3.
- rna_barcode_count_r1
- Cellular eGFP RNA barcode count for analyzed biological replicate 1, from source column FlipIn_r1.
- rna_barcode_count_r2
- Cellular eGFP RNA barcode count for analyzed biological replicate 2, from source column FlipIn_r2.
- rna_barcode_count_r3
- Cellular eGFP RNA barcode count for analyzed biological replicate 3, from source column FlipIn_r3.
- activity_ratio_r1
- RNA:plasmid activity ratio for replicate 1 from the source MPRA counts sheet.
- activity_ratio_r2
- RNA:plasmid activity ratio for replicate 2 from the source MPRA counts sheet.
- activity_ratio_r3
- RNA:plasmid activity ratio for replicate 3 from the source MPRA counts sheet.
- activity_ratio_mean
- Mean RNA:plasmid activity ratio across the three analyzed replicates from source column rep_ave.
- mpra_log2fc
- DESeq2 log2 fold change for normalized MPRA RNA activity relative to plasmid DNA for this allele.
- mpra_log2fc_se
- Standard error of mpra_log2fc from the supplied MPRA fold-change result.
- mpra_neg_log10_p_value
- Negative base-10 logarithm of the MPRA activity p-value, as supplied in log10pval.
- mpra_neg_log10_fdr
- Negative base-10 logarithm of the multiple-testing-adjusted MPRA activity p-value, as supplied in log10fdr.
- allelic_fold_change_vs_reference
- Allelic MPRA activity fold change relative to the reference allele; reference rows are 1.
- allelic_log2fc_vs_reference
- Base-2 logarithm of allelic_fold_change_vs_reference, derived for convenience.
- allelic_p_value
- Allelic comparison p-value supplied for the non-reference allele; reference rows are structurally blank.
- is_cre_active_allele
- Whether the allele occurs in the supplied list of MPRA CRE-active alleles (the >1.5 activity list).
- is_allelic_emvar
- Whether the allele occurs in the supplied significant allelic emVar list; the list contains 195 allele rows representing 187 variants.
- emvar_fold_change_ratio
- Allelic fold-change ratio reported in the supplied significant emVar list; blank for alleles not in that list.
- emvar_p_value
- Allelic p-value reported in the supplied significant emVar list; blank for alleles not in that list.
- emvar_category
- Source category for an allele in the significant emVar list, such as significant-enAllele.
- is_cardiac_enhancer
- Whether the allele occurs in the supplied HE_enAlleles cardiac-enhancer overlap list.
- is_heart_dgf
- Whether the allele occurs in the supplied HF_enAlleles heart DNase genomic-footprint overlap list.
- is_both_cardiac_cre
- Whether the allele occurs in the supplied Heart_CRE_enAlleles list for overlap with both cardiac CRE sets.
- is_cardiac_eqtl
- Whether the variant has at least one association in the supplied MPRA_cardiac_eQTL sheet.
- cardiac_eqtl_genes
- Semicolon-separated unique gene symbols or Gencode IDs linked to the variant in cardiac eQTL data.
- cardiac_eqtl_tissues
- Semicolon-separated cardiac tissues represented in the variant's MPRA eQTL associations.
- cardiac_eqtl_min_p_value
- Smallest supplied cardiac eQTL p-value for the variant across genes and tissues.
- cardiac_eqtl_associations
- Semicolon-separated cardiac eQTL records encoded as gene|tissue|p=value|NES=value.
- source_count_metric_anomaly
- Flags a retained result row with at least one zero or nonnumeric value among source plasmid/RNA counts or replicate activity ratios.
- qc_pass
- All rows are present in the paper's final analyzed MPRA result sheets after the reported barcode QC filter.
Quality control
The authors retained oligos with at least 10 unique barcodes, normalized oligo counts for sequencing depth with the DESeq2 median-of-ratios method, estimated RNA-versus-plasmid activity with a DESeq2 Wald test, and used multiple-testing correction for activity and allelic skew. The processed table was restricted to the 14,213 allele-level rows present in both the supplied MPRA fold-change and allelic-fold-change result sheets, with matching count and sequence records; 19 count-only records lacking a final fold-change result were excluded. No significance filter was applied, so inactive alleles remain. Thirteen retained source rows contain a zero or nonnumeric (#DIV/0!) value in at least one replicate count/activity field; nonnumeric values are blanked and source_count_metric_anomaly flags those rows because the corresponding final result sheets contain analyzed values.
Curation notes
The article is an open-access Research Square preprint (posted 2026-01-07). The paper's key-resources table contains the literal placeholder GEO LINK for MPRA and SNP Bind-n-Seq, with no accession or actual GEO URL; the author-provided supplementary MPRA workbooks are therefore the genuine packaged data source. Supplementary Data 3 provides the library, counts, activity results, and CRE overlap lists; Supplementary Data 4 provides allelic activity results and the significant emVar list; Supplementary Data 5 contributes the MPRA cardiac eQTL sheet. The paper text reports 14,114 barcode-filtered oligos, whereas the supplied result sheets contain 14,213 rows and the count sheet contains 14,232 rows; this package follows the supplied final result sheets, excludes the 19 count-only rows, and documents the discrepancy. Source result labels Alt/Alt-1/Alt-2 were normalized only for joins to count/library labels Non-Ref/Non-Ref-1/Non-Ref-2; the reported label and original element ID remain visible. The model is a genetically modified HEK293-derived reporter context rather than a cardiomyocyte or cardiac tissue assay.