CHD noncoding de novo variant REF/ALT lentiMPRA
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart diseaseA lentiviral MPRA tested 6,590 prioritized congenital-heart-disease noncoding de novo variants as matched 171-bp reference and alternate allele oligos in human iPSC-derived cardiomyocytes. The library was applied at differentiation day 17 and assayed on day 24 with four biological DNA and RNA replicates; the processed table contains the 4,210 intact REF–ALT pairs that passed the published coverage filter.
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
Each prioritized ncDNV was synthesized as a reference/alternate pair containing 171 bp of genomic sequence centered on the variant and a unique 15-bp barcode. Barcoded oligos were cloned into a lentiviral reporter with the sequence upstream of a minimal promoter/GFP cassette and the barcode in the reporter 3′ UTR. Day 17 iPSC-CMs received the library and reporter RNA plus genomic DNA were sequenced on day 24. The source library also contained negative, positive, and shared mutagenesis controls; controls are not included in this variant-pair table.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (64 of 64)
| Row | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 11 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 13 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 15 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 29 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 30 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 34 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 35 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 36 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 37 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 38 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 39 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 40 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 41 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 42 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 43 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 44 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 45 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 46 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 47 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 48 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 49 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 50 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 64 definitions
- variant_id
- Publisher unique identifier for the CHD de novo variant.
- mpra_region_hg38
- 171-bp MPRA reference interval centered on the variant, reported on GRCh38/hg38.
- variant_chromosome
- Variant chromosome from the source CHD annotation.
- variant_start_hg38
- Variant start coordinate from the source CHD annotation.
- variant_end_hg38
- Variant end coordinate from the source CHD annotation.
- reference_allele
- Reference allele or reference indel sequence.
- alternate_allele
- Alternate allele or alternate indel sequence.
- nearest_gene
- Nearest gene assigned by the source annotation.
- nearest_gene_distance
- Source distance from the variant to the nearest gene.
- category_heartENN
- Indicator or score category showing HeartENN-based prioritization.
- category_fetal_enhancer
- Indicator for overlap with a human fetal cardiac enhancer.
- category_gene_TSS
- Source annotation for proximity to a prioritized CHD-gene transcription start site.
- heartENN_score
- HeartENN prioritization score from the source annotation.
- EpiCard
- EpiCard score reported for the variant in the source workbook.
- coding
- Source coding-variant indicator; the retained MPRA variants are noncoding.
- ref_dna_count_rep1
- Raw reference-allele genomic-DNA reporter count for replicate 1.
- ref_dna_count_rep2
- Raw reference-allele genomic-DNA reporter count for replicate 2.
- ref_dna_count_rep3
- Raw reference-allele genomic-DNA reporter count for replicate 3.
- ref_dna_count_rep4
- Raw reference-allele genomic-DNA reporter count for replicate 4.
- ref_rna_count_rep1
- Raw reference-allele reporter-RNA count for replicate 1.
- ref_rna_count_rep2
- Raw reference-allele reporter-RNA count for replicate 2.
- ref_rna_count_rep3
- Raw reference-allele reporter-RNA count for replicate 3.
- ref_rna_count_rep4
- Raw reference-allele reporter-RNA count for replicate 4.
- ref_dna_fpm_rep1
- Publisher-normalized reference DNA count in fragments per million for replicate 1.
- ref_dna_fpm_rep2
- Publisher-normalized reference DNA count in fragments per million for replicate 2.
- ref_dna_fpm_rep3
- Publisher-normalized reference DNA count in fragments per million for replicate 3.
- ref_dna_fpm_rep4
- Publisher-normalized reference DNA count in fragments per million for replicate 4.
- ref_rna_fpm_rep1
- Publisher-normalized reference RNA count in fragments per million for replicate 1.
- ref_rna_fpm_rep2
- Publisher-normalized reference RNA count in fragments per million for replicate 2.
- ref_rna_fpm_rep3
- Publisher-normalized reference RNA count in fragments per million for replicate 3.
- ref_rna_fpm_rep4
- Publisher-normalized reference RNA count in fragments per million for replicate 4.
- ref_log2_activity_rep1
- Publisher reference-allele log2 RNA/DNA activity score for replicate 1.
- ref_log2_activity_rep2
- Publisher reference-allele log2 RNA/DNA activity score for replicate 2.
- ref_log2_activity_rep3
- Publisher reference-allele log2 RNA/DNA activity score for replicate 3.
- ref_log2_activity_rep4
- Publisher reference-allele log2 RNA/DNA activity score for replicate 4.
- ref_mean_log2_activity
- Publisher mean reference-allele log2 RNA/DNA activity score.
- alt_dna_count_rep1
- Raw alternate-allele genomic-DNA reporter count for replicate 1.
- alt_dna_count_rep2
- Raw alternate-allele genomic-DNA reporter count for replicate 2.
- alt_dna_count_rep3
- Raw alternate-allele genomic-DNA reporter count for replicate 3.
- alt_dna_count_rep4
- Raw alternate-allele genomic-DNA reporter count for replicate 4.
- alt_rna_count_rep1
- Raw alternate-allele reporter-RNA count for replicate 1.
- alt_rna_count_rep2
- Raw alternate-allele reporter-RNA count for replicate 2.
- alt_rna_count_rep3
- Raw alternate-allele reporter-RNA count for replicate 3.
- alt_rna_count_rep4
- Raw alternate-allele reporter-RNA count for replicate 4.
- alt_dna_fpm_rep1
- Publisher-normalized alternate DNA count in fragments per million for replicate 1.
- alt_dna_fpm_rep2
- Publisher-normalized alternate DNA count in fragments per million for replicate 2.
- alt_dna_fpm_rep3
- Publisher-normalized alternate DNA count in fragments per million for replicate 3.
- alt_dna_fpm_rep4
- Publisher-normalized alternate DNA count in fragments per million for replicate 4.
- alt_rna_fpm_rep1
- Publisher-normalized alternate RNA count in fragments per million for replicate 1.
- alt_rna_fpm_rep2
- Publisher-normalized alternate RNA count in fragments per million for replicate 2.
- alt_rna_fpm_rep3
- Publisher-normalized alternate RNA count in fragments per million for replicate 3.
- alt_rna_fpm_rep4
- Publisher-normalized alternate RNA count in fragments per million for replicate 4.
- alt_log2_activity_rep1
- Publisher alternate-allele log2 RNA/DNA activity score for replicate 1.
- alt_log2_activity_rep2
- Publisher alternate-allele log2 RNA/DNA activity score for replicate 2.
- alt_log2_activity_rep3
- Publisher alternate-allele log2 RNA/DNA activity score for replicate 3.
- alt_log2_activity_rep4
- Publisher alternate-allele log2 RNA/DNA activity score for replicate 4.
- alt_mean_log2_activity
- Publisher mean alternate-allele log2 RNA/DNA activity score.
- alt_minus_ref_log2_activity
- Publisher alternate-minus-reference log2 activity difference.
- pvalue
- Publisher paired-test P value for the REF–ALT comparison.
- qvalue
- Publisher Benjamini–Hochberg adjusted P value for the REF–ALT comparison.
- active_ref
- Publisher activity call for the reference allele: 1 active and 0 inactive.
- active_alt
- Publisher activity call for the alternate allele: 1 active and 0 inactive.
- effect_class_code
- Publisher effect code: 1 MPRA-DA, 2 MPRA-IA, 0 MPRA-NS.
- effect_class
- Readable publisher effect class: decreased activity, increased activity, or no significant change.
Quality control
The paper retained regions with FPM ≥ 20 coverage and reported 4,210 intact REF–ALT pairs (77.5% of the designed library) with four-replicate Pearson r > 0.86. The package retains exactly the 4,210 publisher differential-analysis pairs, requires both REF and ALT members and complete raw-count/FPM joins, and preserves the publisher's active flags, P values, Benjamini–Hochberg q values, effect classes, and 0.58 absolute log2-fold-change threshold encoded by those classes. MPRA-NS pairs are retained as non-significant controls. Two duplicated names occur in the deposited CHD raw-count file; the last record was used, which matches the publisher FPM table.
Curation notes
The variant table is one row per intact REF–ALT pair and excludes the library's negative/positive/shared controls. It reports source uniqueVarID values rather than dbSNP rsIDs because these are rare de novo variants. The source workbook labels the variant annotation/differential-analysis coordinates hg38; the paper's general read-mapping method mentions hg19, so the package uses GRCh38 for the public variant annotation coordinates and leaves published interval strings unchanged.