Allelic variant lentiMPRA in primary human mid-gestation cortical cells
Massively parallel characterization of regulatory elements in the developing human cortexA 270-bp variant library centered on brain QTLs and psychiatric-disorder-associated variants was tested in GW18 primary human cortical cells with reference and alternative alleles. Allelic enhancer activity is represented by the alternative/reference RNA/DNA ratio and limma differential-activity statistics.
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.
Perturbation & assay details
Basal / Untreated; GW18 primary human cortical cells
The variant library used 270-bp inserts centered on each variant, a 31-bp minimal promoter, and a 15-bp random barcode in a lentiviral reporter. Reference and alternative alleles were assayed after genomic integration; allele-specific activity is reported as the alternative/reference RNA/DNA ratio, with limma logFC, P value, and adjusted P value supplied by the source analysis.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 35 definitions
- variant_id
- Variant rsID from the source library.
- variant_chromosome
- Chromosome of the variant in GRCh38.
- variant_position
- GRCh38 position of the variant.
- insert_id
- Source identifier for the 270-bp reporter insert containing the variant.
- insert_start
- Source start coordinate of the reporter insert.
- insert_end
- Source end coordinate of the reporter insert.
- insert_length_bp
- Derived insert length in base pairs, calculated as insert_end minus insert_start.
- alt_ref_ratio
- Source alternative-allele activity divided by reference-allele activity.
- log2_alt_ref_ratio
- Derived base-2 logarithm of alt_ref_ratio.
- alt_activity_rna_dna_ratio
- Source CPM-normalized RNA/DNA activity for the alternative allele.
- ref_activity_rna_dna_ratio
- Source CPM-normalized RNA/DNA activity for the reference allele.
- alt_is_active
- Source active/inactive call for the alternative allele.
- ref_is_active
- Source active/inactive call for the reference allele.
- limma_logFC
- Source limma log2 fold-change for the alternative allele relative to the reference allele.
- limma_p_value
- Source limma nominal P value for the allelic activity test.
- limma_adjusted_p_value
- Source multiple-testing-adjusted limma P value.
- effect_direction
- Derived direction of the limma effect: increased, decreased, or no_effect.
- reported_da_1pct
- Derived 1% FDR differential-activity flag: adjusted P <0.01 and absolute limma logFC >0.5.
- reported_da_10pct
- Derived 10% FDR differential-activity flag: adjusted P <0.10 and absolute limma logFC >0.5.
- atac_cell_types
- Semicolon-separated cell types whose ATAC-seq annotations overlap the variant insert.
- da_cell_types
- Semicolon-separated cell types whose differentially accessible annotations overlap the variant insert.
- qtl_sources
- Semicolon-separated QTL datasets in which the variant or linked variant is annotated.
- gwas_ld_traits
- Semicolon-separated psychiatric or neurological GWAS traits linked by LD in the source annotations.
- closest_cross_disorder_gene
- Closest cross-disorder differentially expressed gene name from the source annotation.
- closest_cross_disorder_distance_bp
- Distance in base pairs to the closest cross-disorder differentially expressed gene.
- qtl_target_id
- Source identifier of a predicted QTL target gene.
- qtl_target_name
- Source name of a predicted QTL target gene.
- qtl_target_tpm_mean
- Source mean TPM expression for the predicted QTL target gene.
- loop_target_genes
- Unique promoter target genes aggregated from source chromatin-loop annotations.
- abc_target_genes
- Unique target gene names from Activity-by-Contact annotations.
- motifbreakr_gene
- Transcription-factor gene whose motif is predicted to be altered by the allele, from motifbreakR.
- motifbreakr_effect_size
- Source motifbreakR effect-size annotation.
- motifbreakr_effect
- Source motifbreakR qualitative effect annotation.
- qtl_conservation
- Source conservation score for the variant/QTL annotation.
- insert_conservation_mean
- Source mean evolutionary conservation score for the full reporter insert.
Quality control
The supplemental methods required merged reads with a 270M CIGAR, base quality >=30, barcode Shannon entropy >0.5, barcode observation >=3 times with >=90% assignment to the same insert, >=10 unique barcodes per insert, and >=40 total DNA barcodes. DNA/RNA counts were CPM-normalized; variant activity was computed from alternative and reference RNA/DNA ratios, and allelic effects were tested with limma including batch terms. Data S2 contains 15,911 primary variant rows; 15,335 rows with finite alternative/reference activity and limma statistics were retained, while 576 rows missing one or more required numeric values were excluded. The processed reported_da flags use adjusted P <0.01 or <0.10 and absolute limma logFC >0.5; this reproducibly gives 132 primary variants at 1% FDR and 163 at 10% FDR, consistent with the reported directional totals.
Curation notes
This table contains the QC-passed allelic reporter results, not the upstream GWAS/QTL candidate list. The biosample is represented at the cerebral-cortex tissue level because the primary assay contains mixed cortical cell types. Source rows lacking finite allele activities or limma statistics were excluded. The paper describes a fold-change cutoff in prose; the supplied source logFC and the reported primary-cell counts are reproduced with absolute limma logFC >0.5, so that explicit reproducible rule is used for reported_da_1pct and reported_da_10pct.