A barcode-tagged episomal oligo library containing both alleles of 5,254 PD-related or PARK-gene-associated SNPs (10,484 reported elements plus controls) was transfected into HEK293 cells in three technical replicates. MPRA activity was quantified from aggregated cDNA/DNA barcode counts and allele-specific differences were tested with mpralm; the processed table contains the 34 rows reported in Supplementary Table 7.
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.
Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0045
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The authors synthesized 200-bp genomic sequences centered on each SNP with 15-bp flanking adapter sequences, added unique 20-bp barcodes by two-stage low-cycle PCR, and cloned the library into pMPRA1/pMPRAdonor2 upstream of a minimal promoter and luciferase open reading frame. The competent library was transfected with Lipofectamine-3000; DNA and RNA were harvested 24 h later, cDNA and DNA barcodes were sequenced on Illumina HiSeq X, and activity was estimated from aggregated RNA/DNA barcode counts. The MPRA was performed in three technical replicates.
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 · 43 definitions
variant_id
rsID of the tested SNP.
source_table_7_row
Excel row number in the authors’ Supplementary Table 7.
ld_tag_snp
GWAS tag or representative SNP when the tested SNP was nominated through PD-GWAS linkage disequilibrium; otherwise the source placeholder.
mapped_gene
GWAS or other mapped gene(s) reported for the tested variant.
nomination_category
Source nomination category, such as PDGWAS_LD, PARK_eQTL, or PARK_intragenic.
library_region_hg38
200-bp genomic region surrounding the tested SNP, as listed in Supplementary Table 1.
chromosome
Chromosome for the hg38 coordinate.
position_hg38
SNP coordinate on the GRCh38/hg38 reference assembly.
ref_allele
Reference allele represented in the MPRA library.
alt_allele
Alternate allele represented in the MPRA library.
higher_activity_allele
Allele inferred from logFC sign: alternate for positive logFC and reference for negative logFC.
logFC
mpralm log fold change in activity between the alternate and reference alleles; source interpretation assigns positive values to higher alternate-allele activity.
AveExpr
mpralm average expression/activity statistic.
t_statistic
mpralm t statistic for the allele-specific RNA count difference.
mpralm B statistic, the log-odds of differential activity.
general_enhancer
Source general-enhancer call from Supplementary Table 7 (Yes/No).
general_enhancer_oligo_count
Number of corresponding allele rows found for this variant in Supplementary Table 6.
general_allele1_mean_ratio
Mean DNA-normalized activity ratio for source allele1 rows in Supplementary Table 6; source allele labels are not forced to ref/alt.
general_allele2_mean_ratio
Mean DNA-normalized activity ratio for source allele2 rows in Supplementary Table 6; source allele labels are not forced to ref/alt.
general_allele1_median_ratio
Median DNA-normalized activity ratio for source allele1 rows in Supplementary Table 6.
general_allele2_median_ratio
Median DNA-normalized activity ratio for source allele2 rows in Supplementary Table 6.
general_allele1_z_score
General-enhancer z-score for source allele1 rows in Supplementary Table 6.
general_allele2_z_score
General-enhancer z-score for source allele2 rows in Supplementary Table 6.
mean_DR_score
Mean depletion-rank score for the variant from Supplementary Table 9.
haploreg_promoter_marks
HaploReg promoter histone-mark annotation from Supplementary Table 11.
haploreg_enhancer_marks
HaploReg enhancer histone-mark annotation from Supplementary Table 11.
haploreg_DNase
HaploReg DNase/open-chromatin annotation from Supplementary Table 11.
haploreg_protein_binding
HaploReg protein-binding annotation from Supplementary Table 11.
haploreg_motif_changes
HaploReg motif-change annotation from Supplementary Table 11.
haploreg_GRASP_QTL
HaploReg GRASP QTL-hit annotation from Supplementary Table 11.
haploreg_selected_eQTL
HaploReg selected-eQTL-hit annotation from Supplementary Table 11.
haploreg_gene_annotation
HaploReg GENCODE gene/region annotation from Supplementary Table 11.
dbSNP_annotation
HaploReg/dbSNP functional annotation from Supplementary Table 11.
tfbs_high_confidence_count
Count of FABIAN TFBS predictions with absolute score at least 0.8.
tfbs_high_confidence_effects
Semicolon-separated TF:score values from FABIAN predictions with absolute score at least 0.8; positive scores indicate increased predicted binding and negative scores weakened binding.
putative_target_gene_count
Number of unique putative target genes assigned by the authors’ CoDeS3D analysis across GTEx tissues.
putative_target_genes
Semicolon-separated unique putative target genes from Supplementary Table 12.
putative_target_interaction_types
Semicolon-separated CoDeS3D interaction types represented for the variant.
reference_sequence_200bp
Reference-allele 200-bp library insert sequence, with the 15-bp 5’ and 3’ library adapters removed.
alternate_sequence_200bp
Alternate-allele 200-bp library insert sequence, with the 15-bp 5’ and 3’ library adapters removed.
Quality control
The authors trimmed and aligned oligonucleotide reads to the designed element library, required barcode representation across all three technical replicates, and omitted elements represented by fewer than 5 barcodes. Barcode composition/frequency correlations between technical replicates were r = 0.69–0.96; 8,849 of 10,496 elements were captured and 8,548 mapped to at least 5 unique barcodes. General enhancers were called at a z-score of at least 3. Allele-specific effects were tested with mpralm using normalization and the corr_groups model; adjusted p-value < 0.05 was the active threshold and 0.05–0.10 was designated suggestive. The processed table retains the 34 source rows in Supplementary Table 7, labels the 27 active and 7 suggestive results, and applies no additional statistical filtering beyond requiring finite source statistics and valid paired library sequences.
Curation notes
This is the paper’s single MPRA condition; the KOLF2.1J CRISPR editing and RNA-seq validation are not MPRA and were not represented as a separate experiment. The publication reports 27 allele-specific enhancers at FDR < 0.05, while Supplementary Table 7 also retains seven suggestive rows at 0.05 <= FDR < 0.10; all 34 are included and explicitly classified. Coordinates and paired sequences were joined from Supplementary Table 1, while general activity and annotations were joined or aggregated from Supplementary Tables 6 and 9–12. Some suggestive rows lack Table 9/11 annotation because those source tables focus on the 27 significant allele-specific elements. The authors state that raw MPRA output is available on request, so no raw sequencing reads or barcode-level count files are included.