An episomal hSTARR-seq library tested 198-bp sequences carrying common European haplotypes across liver- and hepatocyte-regulatory regions containing CAD/MI GWAS SNPs. The library was transfected in triplicate into HepG2 cells, and input DNA versus reporter RNA sequencing was used to identify allele-specific enhancer 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.
Organism
Human
Taxonomy ID
NCBITaxon:9606
Biosample
CVCL:0027
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The 230-bp synthesized inserts contained a 198-bp SNP-containing enhancer sequence, a 2-bp 5-prime barcode, and 15-bp Illumina adapter sequences, cloned into the hSTARR-seq_ORI plasmid (Addgene #99296). The plasmid library was transfected into 7 x 10^7 HepG2 cells in triplicate and harvested 24 h later; poly(A) RNA was reverse-transcribed with UMI primers, amplified through the reporter junction, and sequenced on a NextSeq 500 with paired-end 75-cycle dual-index runs. Reads were mapped to synthesized oligos, deduplicated with UMI-tools, and analyzed with QuASAR-MPRA and Fisher's method for allele-specific expression.
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 · 26 definitions
element_id
Generated stable identifier for a retained STARR-seq result row.
regulatory_regions
Table S6 regulatory-region identifier(s) associated with the SNP group.
snp_ids
CAD/MI SNP rsIDs in the reported allele-specific result group, separated by semicolons.
snp_count
Number of unique SNPs in the result group.
variant_coordinates_hg19
SNP coordinates in hg19 formatted as rsID=chr:position.
ref_alleles
Reference alleles from Table S6, formatted as rsID=allele.
alt_alleles
Alternate alleles from Table S6, formatted as rsID=allele.
ref_allele_counts_eur
Reference-allele counts in the European 1000 Genomes haplotype set reported in Table S6.
alt_allele_counts_eur
Alternate-allele counts in the European 1000 Genomes haplotype set reported in Table S6.
ref_allele_frequencies_eur
Reference-allele frequencies in the European 1000 Genomes haplotype set reported in Table S6.
alt_allele_frequencies_eur
Alternate-allele frequencies in the European 1000 Genomes haplotype set reported in Table S6.
minor_allele_frequencies_eur
Minor-allele frequencies reported in Table S6 for the European haplotype set.
haplotype_1_alleles
Alleles carried at the listed SNPs by synthesized haplotype 1, formatted as rsID=allele.
haplotype_2_alleles
Alleles carried at the listed SNPs by synthesized haplotype 2, formatted as rsID=allele.
haplotype_3_alleles
Alleles carried at the listed SNPs by synthesized haplotype 3, formatted as rsID=allele.
haplotype_4_alleles
Alleles carried at the listed SNPs by synthesized haplotype 4, formatted as rsID=allele.
haplotype_5_alleles
Alleles carried at the listed SNPs by synthesized haplotype 5, formatted as rsID=allele; blank when not present in Table S6.
closest_gene
Closest gene annotation from Table S22.
hic_target_genes
Promoter Capture Hi-C target-gene annotation from Table S22.
eqtl_target_genes
Liver cis-eQTL target-gene annotation from Table S22.
allele_specific_activity_p_value
P value reported in Table S22 for haplotype-specific STARR-seq activity.
allele_specific_activity_fdr
FDR reported in Table S22 for haplotype-specific STARR-seq activity.
activity_call
Qualitative call that the result passed the packaged allele-specific activity threshold.
library_design_match
TRUE when every SNP in the result group was found in Table S6; FALSE otherwise.
mapping_status
Status of joining the S22 result group to Table S6, including multiple-region or missing-record cases.
qc_pass
TRUE for rows retained after the numeric FDR < 0.05 filter.
Quality control
The study mapped reads to the synthesized oligo library with Bowtie, removed PCR duplicates with UMI-tools, and called allele-specific reporter expression using QuASAR-MPRA followed by Fisher's method. For this package, rows were retained only when Table S22 contained a numeric FDR < 0.05; all 177 reported rows passed. Retained rows were joined to Table S6 by rsID for coordinates, alleles, European allele frequencies, and synthesized haplotype alleles. The source result table does not provide signed effect sizes or RNA/DNA counts, so activity direction was not inferred.
Curation notes
Table S22 contains 177 significant result rows representing 212 unique CAD/MI SNPs; 28 rows contain multi-SNP groups. Four groups map to more than one Table S6 regulatory-region record and are retained with all mapped regions. rs77911820 is reported in Table S22 but is absent from Table S6, so its library design fields are blank and mapping_status records the discrepancy. Table S22 reports significance but not signed RNA/DNA activity ratios or read counts; no effect direction was added.