Experiment / E9JZ3L5K9Episomal Plasmid MPRA

ENIGMA cortical-structure variant MPRA in phNPCs, Wnt-stimulated condition

Massively parallel assessment of gene regulatory activity at human cortical structure associated variants

Both alleles of 9,052 cortical-structure-associated variants from 198 ENIGMA GWAS loci were tested as 150-bp episomal reporter elements in primary human neural progenitor cells after Wnt pathway stimulation. The table combines allele-level regulatory activity, CHIR-condition allelic effects, and the published stimulation-versus-vehicle comparisons where available.

Download processed table (CSV)Raw source data API documentation

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: GRCh37
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

2.5 µM CHIR99021 (CHIR; Wnt stimulation) for 48 h after 24 h post-transfection

Both alleles of each selected SNP-centered 150-bp human reference sequence were synthesized and cloned upstream of a minimal promoter driving luciferase followed by a random 20-bp barcode. The pooled plasmid library was transfected into 16 biological replicates of phNPCs; after 24 h, cells received 7 µL of 2.5 µM CHIR99021 per well and were harvested 48 h later for barcode DNA-seq and RNA-seq. Activity and allelic effects were analyzed with MPRAnalyze v1.9.1; DMSO vehicle samples were assayed in parallel for the condition-dependent columns.

Processed data

50 rows per page. Click a cell to inspect its full value.

Search table valuesFilter columnOperatorValue

Visible columns (40 of 40)

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Page 1 · 50 rows · More results available

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; ENIGMA_GWAS identifies cortical-structure-associated GWAS variants.
locus_id: ENIGMA GWAS locus identifier.
variant_id: dbSNP 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: ENIGMA GWAS locus label for the tested variant.
chromosome: Chromosome label from the source workbook.
position_reference_genome: 1-based variant position in GRCh37/hg19.
condition: MPRA biological condition represented by this experiment.
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.
gwas_thickness_p_lt_5e_8_count: Number of cortical-thickness associations at P < 5 × 10^-8.
gwas_surface_area_p_lt_1e_5_count: Number of cortical-surface-area associations at P < 1 × 10^-5.
gwas_surface_area_p_lt_5e_8_count: Number of cortical-surface-area associations at P < 5 × 10^-8.
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 CHIR-condition allelic effect.
allelic_p_value: P-value for the CHIR-condition allelic effect.
allelic_fdr: Benjamini–Hochberg adjusted P-value for the CHIR-condition 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 ENIGMA rows.
higher_accessibility_allele: Higher-accessibility caQTL allele; blank for ENIGMA rows.
condition_activity_statistic: Squared condition-dependent activity statistic (logFC/se)^2.
condition_activity_log2fc_stim_vs_vehicle: Condition-dependent activity log2 fold-change for CHIR 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 CHIR 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 supplementary stimulated activity sheet is post-QC and contains 17,848 rows, of which 927 are called active at FDR < 0.1 and 16,921 inactive. The package additionally required non-empty identifiers, finite activity statistics, and active/inactive status; all 17,848 rows passed. For the stimulation-versus-vehicle comparative analysis, the authors excluded one replicate with a DNA library-size correction factor below 0.10. A source p-value of 0 is retained as the authors’ underflow indicator (<2.225074 × 10^-308).

Curation notes

This is the ENIGMA stimulation sheet (Supplementary Table 3c-style activity results) and uses the source legend's hg19 coordinates. The activity rows include inactive elements so researchers can compare active calls against the tested background; inactive is not a QC failure. The condition-dependent columns are repeated from the authors' separate interaction sheets and are blank when a variant was not included in that test. 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.

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50