This table contains the paper's separately reported caQTL subset: both alleles of 502 chromatin-accessibility-associated SNPs in 150-bp sequences from primary human neural progenitor chromatin-accessible peaks. The publication reports this caQTL analysis without a vehicle-versus-CHIR condition label, so it is represented as its own analytical experiment and should not be interpreted as a CHIR-specific result.
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
CL:0011020
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Perturbation not reported.
Each 150-bp reference-genome sequence centered on a bi-allelic caQTL SNP was synthesized with both alleles, cloned upstream of a minimal promoter driving luciferase followed by a random 20-bp barcode, and assayed in primary human neural progenitor cells. Barcode DNA input and RNA output were sequenced; activity was modeled with MPRAnalyze v1.9.1 and the source workbook labels these caQTL coordinates as hg38/GRCh38.
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 · 40 definitions
element_id
Unique dataset/locus/variant/tested-allele identifier generated for this table row.
dataset
Analytical MPRA subset; phNPC_caQTL identifies the chromatin-accessibility QTL library.
locus_id
GWAS locus identifier when supplied; blank for the caQTL subset.
variant_id
Variant or source SNP identifier from the supplementary workbook.
tested_allele
Allele represented by the activity row.
reference_allele
Reference allele in the source allelic-effect result, when reported.
alternative_allele
Tested alternative allele in the source allelic-effect result, when reported.
peak_or_locus
Source caQTL chromatin-accessibility peak location or ENIGMA locus label.
chromosome
Chromosome label from the source workbook.
position_reference_genome
1-based variant position in the experiment's declared reference assembly.
condition
Condition label; the caQTL source sheet is condition-agnostic.
regulatory_activity_mad_score
Median absolute deviation score for activity relative to negative controls.
regulatory_activity_alpha
MPRAnalyze transcription-rate estimate for the element allele.
regulatory_activity_p_value
P-value for the regulatory activity test.
regulatory_activity_fdr
Benjamini–Hochberg adjusted P-value for regulatory activity.
regulatory_activity_status
Source activity call: active or inactive.
gwas_thickness_p_lt_1e_5_count
Number of cortical-thickness associations at P < 1 × 10^-5; blank for caQTL rows.
gwas_thickness_p_lt_5e_8_count
Number of cortical-thickness associations at P < 5 × 10^-8; blank for caQTL rows.
gwas_surface_area_p_lt_1e_5_count
Number of cortical-surface-area associations at P < 1 × 10^-5; blank for caQTL rows.
gwas_surface_area_p_lt_5e_8_count
Number of cortical-surface-area associations at P < 5 × 10^-8; blank for caQTL rows.
allelic_log2fc_alt_vs_ref
Source log2 fold-change for the tested alternative allele relative to the reference allele.
allelic_average_log2_expression
Average log2 expression used in the allelic model.
allelic_moderated_t
Moderated t-statistic for the allelic effect.
allelic_p_value
P-value for the allelic effect.
allelic_fdr
Benjamini–Hochberg adjusted P-value for the allelic effect.
allelic_B_log_odds
B-statistic/log-odds that the allele is differentially expressed.
emvar
Source binary call indicating an expression-modulating variant/allelic effect.
caqtl_beta
Published caQTL effect size; blank for non-caQTL rows.
higher_accessibility_allele
Allele associated with higher chromatin accessibility in the caQTL result.
condition_activity_statistic
Squared condition-dependent activity statistic (logFC/se)^2; blank when not reported.
condition_activity_log2fc_stim_vs_vehicle
Condition-dependent activity log2 fold-change for stimulation versus vehicle.
condition_activity_p_value
P-value for the condition-dependent activity test.
condition_activity_fdr
Benjamini–Hochberg adjusted P-value for condition-dependent activity.
condition_allelic_log2fc_stim_vs_vehicle
Condition-dependent allelic interaction log2 fold-change for stimulation versus vehicle.
condition_allelic_average_log2_expression
Average log2 expression in the condition-dependent allelic model.
condition_allelic_moderated_t
Moderated t-statistic for the condition-dependent allelic interaction.
condition_allelic_p_value
P-value for the condition-dependent allelic interaction.
condition_allelic_fdr
Benjamini–Hochberg adjusted P-value for the condition-dependent allelic interaction.
condition_allelic_B_log_odds
B-statistic/log-odds for the condition-dependent allelic interaction.
qc_pass
TRUE for rows retained after the documented source and package-level QC checks.
Quality control
The authors trimmed adapters with cutadapt v4.1, retained perfectly matched 20-bp barcodes, filtered barcode observations with DNA or RNA counts below 5, required at least 5 unique barcodes per element, removed barcode-level RNA/DNA outliers with boxplot.stats(), removed low-correlation biological replicates (correlations 0.3–0.7), and retained elements represented in at least 10 replicates. The source caQTL result sheet is post-QC; the package additionally retained only rows with non-empty identifiers, finite activity statistics, and an activity status of active or inactive. All 1,316 source rows passed these package checks. A source p-value of 0 is retained as the authors’ underflow indicator (<2.225074 × 10^-308).
Curation notes
The caQTL workbook is explicitly labeled as a separate caQTL dataset and its legend specifies hg38 coordinates, unlike the ENIGMA workbook's hg19 coordinates. No separate caQTL stimulation activity sheet was supplied. Blank ENIGMA and condition-dependent columns are intentional; this table preserves the reported caQTL activity and allelic results without duplicating them into a CHIR experiment. The biological source is primary human neural progenitor cells; CL:0011020 is the generic neural progenitor-cell ontology term because a more specific terminal cell type was not stated.