The same human STARR-seq PGx-eQTL plasmid library was transfected into the A549 lung cancer cell line to test context-dependent enhancer activity. Cells were exposed for 9 h to vehicle, 100 nM hydrocortisone, or 100 nM CORT108297; the table contains the 94 published SNP–gene loci with GR-dependent STARR-seq activity calls.
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:0023
Reference genome
hg19
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Vehicle (0.1% DMSO + 0.1% ethanol), 100 nM hydrocortisone + 0.1% DMSO, or 100 nM CORT108297 + 0.1% ethanol for 9 h
Human STARR-seq-ORI plasmid (Addgene #99296) carried PCR-amplified PGx-eQTL peak fragments extended by approximately ±500 bp, with an FKBP5 enhancer positive control. Active inserts self-transcribed from the reporter, were enriched by RT-PCR, and were quantified by paired-end sequencing; the same library was tested under vehicle, hydrocortisone, and CORT108297 conditions.
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 · 24 definitions
element_id
Stable row identifier combining the reported rsID, target gene, and PGx drug context
variant_id
Reported dbSNP rs identifier
target_gene
PGx-eQTL target gene
reported_drug_context
Drug context of the parent PGx-eQTL association (Cortisol or C297)
reference_allele
Reference allele reported in Supplementary Data 2
alternate_allele
Alternate allele reported in Supplementary Data 2
chromosome
hg19 chromosome containing the cloned locus
variant_position_hg19
Unique hg19 VCF position matched by chromosome, interval, and REF/ALT; blank when not uniquely resolved
variant_position_candidates_hg19
All matching VCF positions when the interval and REF/ALT match more than one position
region_start_hg19
Start of the cloned PGx-eQTL interval in hg19
region_end_hg19
End of the cloned PGx-eQTL interval in hg19
region_length_bp
Inclusive length of the cloned interval in base pairs
chip_reproducible_fdr01
Source GR ChIP-seq reproducibility call at FDR 0.01
chip_reproducible_fdr05
Source GR ChIP-seq reproducibility call at FDR 0.05
starr_gr_dependent_activity
Source call for GR-dependent STARR-seq activity; all retained rows are Yes
chromhmm_state
Predicted ChromHMM chromatin state for the locus
dnase_gm12878
Whether the source table reports ENCODE GM12878 DNase overlap
de_novo_snp_ld_status
Source statement about de novo STARR-seq SNP discovery and LD with the genotyped SNP
qc_status
Package QC status; rows were retained by the published STARR activity-call filter
starr_cortisol_signal_a549
Published qualitative A549 STARR-seq cortisol signal, listing named SNPs when available
starr_cortisol_variant_direction_a549
Parsed direction for this row's rsID in the A549 cortisol signal, or a summary category when not explicitly named
starr_c297_signal_a549
Published qualitative A549 STARR-seq C297 signal, listing named SNPs when available
starr_c297_variant_direction_a549
Parsed direction for this row's rsID in the A549 C297 signal, or a summary category when not explicitly named
source_supplement_row
Original Excel row number in Supplementary Data 2
Quality control
The authors reported greater than 90% mapping across samples and replicate r² ≥ 0.9. Adapter and universal plasmid sequence were removed, reads were aligned to GRCh37/hg19 with BWA-MEM, MAPQ ≥30 reads were retained, allele/locus counts were called with bcftools mpileup and HTSeq, and indels, multiallelic variants, and variants with counts <20 were removed. For this package, only the 94 of 134 Supplementary Data 2 rows marked Yes for GR-dependent STARR-seq activity were retained.
Curation notes
The source workbook provides qualitative STARR-seq activity/direction strings rather than numeric count or log2 fold-change values; those strings are retained verbatim in the table and the parsed direction is only assigned when the row's rsID is explicitly named. Variant positions were recovered by matching REF/ALT and cloned interval against the deposited VCF when unique; 11 retained rows have no unique match and 8 have multiple candidate matches, which are left blank or listed in the candidate column. A549 is represented by Cellosaurus accession CVCL:0023.