An episomal allele-comparison MPRA tested 4,608 blood-pressure-associated variants as 135-bp genomic fragments, with reference and alternative alleles represented by 25 barcodes per allele, in 21-day human iPSC-derived cardiomyocytes. Five TagSeq biological replicates were collected 48 h after transfection against a shared plasmid DNA input library; this table contains the 1,788 variants with significant differential allele activity.
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.
Each reference and alternative allele was centered in a 135-bp genomic context and represented by 25 unique 11-bp barcodes in an episomal plasmid containing a CMV minimal-promoter/GFP reporter. The pool also contained 335 random negative-control sequences and six known regulatory positive-control variants. Five cardiomyocyte TagSeq replicates and one plasmid DNA input were sequenced as single-end 50-bp HiSeq 2500 libraries; MPRAnalyze quantified RNA-versus-DNA activity and allele-differential effects.
Processed data
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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 · 39 definitions
variant_id
dbSNP rs identifier for the tested variant.
published_variant_id_hg38
Variant identifier reported by the source MPRA results as an hg38 identifier.
chromosome
Chromosome parsed from the source allele notation.
position_grch38
1-based variant coordinate on GRCh38/hg38 from the source allele notation.
reference_allele
Reference allele represented in the tested oligo.
alternative_allele
Alternative allele represented in the tested oligo.
allele_change
Source allele notation in chromosome:position:reference:alternative form.
sentinel_gwas_variant
Sentinel or lead blood-pressure GWAS variant associated with the tested LD locus.
gwas_trait_code
Source trait code: SBP, DBP, or PP.
gwas_trait
Expanded blood-pressure trait label corresponding to gwas_trait_code.
tested_135bp_region
135-bp genomic context used for the MPRA oligo, in the source coordinate notation.
published_oligo_name
Complete oligo identifier reported in Table S1.
ensembl_gene_id
Ensembl gene identifier associated with the source nearest-gene annotation.
nearest_gene
Nearest annotated gene symbol reported by the study.
distance_to_gene_bp
Reported signed distance from the variant to the annotated gene, in base pairs.
log2_fc_ref_minus_alt
MPRAnalyze allelic log2 fold-change reported as reference activity minus alternative activity; positive values indicate higher reference activity and negative values indicate higher alternative activity.
allelic_p_value
P-value for the reference-versus-alternative differential MPRA activity test.
allelic_fdr
False-discovery-rate-adjusted value for the differential MPRA activity test.
allelic_fdr_pass_0_05
Boolean indicating that the published differential MPRA FDR passed the q < 0.05 cutoff.
effect_direction
Direction derived from the sign of log2_fc_ref_minus_alt.
activity_status
Published MPRAnalyze activity call versus the random-sequence background: Active or Not Active.
overlap_other_cell_type
Published overlap of this differential/activity result with the VSMC experiment.
effect_size_rank
Published rank of the variant by allelic effect size.
fdr_rank
Published rank of the variant by allelic FDR.
reference_only_tfbs
Predicted transcription-factor motifs unique to the reference allele, as a comma-separated list.
alternative_only_tfbs
Predicted transcription-factor motifs unique to the alternative allele, as a comma-separated list.
differential_tf_motif_count
Reported signed count of differentially predicted transcription-factor motifs between the two alleles.
eqtl_coronary_artery
Whether the variant overlaps a GTEx coronary-artery eQTL according to the study.
eqtl_atrial_appendage
Whether the variant overlaps a GTEx heart atrial-appendage eQTL according to the study.
eqtl_left_ventricle
Whether the variant overlaps a GTEx heart left-ventricle eQTL according to the study.
eqtl_aorta
Whether the variant overlaps a GTEx aorta eQTL according to the study.
eqtl_tibial_artery
Whether the variant overlaps a GTEx tibial-artery eQTL according to the study.
eqtl_genes_coronary_artery
Comma-separated Ensembl IDs of coronary-artery eQTL target genes reported by the study.
eqtl_genes_atrial_appendage
Comma-separated Ensembl IDs of atrial-appendage eQTL target genes reported by the study.
eqtl_genes_left_ventricle
Comma-separated Ensembl IDs of left-ventricle eQTL target genes reported by the study.
eqtl_genes_aorta
Comma-separated Ensembl IDs of aorta eQTL target genes reported by the study.
eqtl_genes_tibial_artery
Comma-separated Ensembl IDs of tibial-artery eQTL target genes reported by the study.
repeat_masker_class
RepeatMasker classification reported for the tested locus: Repeat or NoRepeat.
source_supplementary_table
Supplementary-table provenance for the row.
Quality control
The authors trimmed and quality-filtered DNA/RNA TagSeq reads with cutadapt, required exact matching of each barcode plus 10 upstream GFP nucleotides, and retained sequences for which at least 50% of barcodes had input-DNA counts >=10 (4,587 variants retained for analysis). MPRAnalyze modeled barcode-specific RNA/DNA activity, used random sequences to define active elements, and tested allele differences against a randomized non-differential-allele null; regulatory variants were called at q < 0.05. Package QC additionally required finite p-value, FDR, and log2 fold-change values, p-value/FDR in [0,1], FDR < 0.05, a valid Table S1 allele/context mapping, and a unique variant/allele key; all 1,788 source rows passed these filters.
Curation notes
The raw GEO archive GSE213558_RAW.tar is included as a compact source archive containing 18 MPRA barcode-count files and related CRISPR prime-editing gene-count files; raw sequence reads are not packaged. The processed table uses published Table S2 MPRA results joined to Table S1 context because the GEO barcode-count files do not provide a public barcode-to-variant mapping. Table S2 is a significant-regulatory-variant subset rather than the full 4,608-element library, so non-significant variants are absent. Activity_status can be Not Active because overall activity versus random controls and allelic differential activity are distinct MPRAnalyze tests. The GEO sample annotation says hg19, whereas the paper's MPRA supplementary identifiers are explicitly hg38 and its chromatin analyses use GRCh38; this package uses GRCh38 for the variant table and preserves the source identifiers.