HT29 colorectal cancer lentiMPRA
Systematic prioritization of functional variants and effector genes underlying colorectal cancer riskLentiviral MPRA of 8,880 GWAS-selected colorectal cancer variants represented by 201-bp genomic probes with reference and alternate alleles in both strands. HT29 colorectal cancer cells were transduced and barcode abundance in DNA and cDNA was used to estimate alternate-versus-reference regulatory activity; the released ST4 table contains the 275-variant union significant in at least one assayed cell line.
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
The pLS-SceI lentiviral MPRA used 201-bp genomic probes (100-bp flanks on each side of the variant), four probe forms per variant (forward and reverse strands for reference and alternate alleles), and random 15-bp probe barcodes. Cells were transduced at a reported viral MOI of 80; three DNA and three RNA replicate libraries were sequenced, with barcode abundance measured in input DNA and cDNA. MPRAflow v2.3.5 performed barcode/probe association and MPRAnalyze v1.12.0 used the scaled DNA-normalized model for allele testing.
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 · 31 definitions
- variant_id
- dbSNP rsID for the tested variant.
- ref_allele
- Reference allele used in the ST4 MPRA result table.
- alt_allele
- Alternate allele used in the ST4 MPRA result table.
- cytoband
- Cytoband from the ST2 variant annotation sheet.
- chromosome
- Chromosome from ST2, written with a chr prefix.
- position_grch37
- 1-based GRCh37/b37 coordinate from ST2.
- position_grch38
- 1-based GRCh38/b38 coordinate from ST2.
- gwas_pvalue
- GWAS association P value from ST2.
- gwas_lead_snp
- Lead GWAS SNP for the locus from ST2.
- gwas_snp
- GWAS SNP or SNP list associated with the row in ST4.
- mpra_logfc_alt_vs_ref
- HT29 MPRA logFC for the alternate construct relative to the reference construct, from ST4.
- mpra_fdr
- HT29 multiple-testing-adjusted FDR for the allele effect, from ST4.
- mpra_significant_fdr_1e-3
- Derived indicator: 1 when the numeric HT29 FDR is <0.001, otherwise 0.
- mpra_annotation_score
- HT29 MPRA annotation score in ST2 (0, 1 or 2) used by the study's integrative scoring scheme.
- eQTL
- ST2 indicator/score for significant eQTL evidence.
- eQTL_direction_consistent
- ST2 indicator for consistency between MPRA and eQTL effect direction.
- SMR
- ST2 indicator/score for SMR evidence.
- SMR_TCGA
- ST2 indicator/score for TCGA SMR evidence.
- Akita
- ST2 Akita score for predicted variant effects on 3D genome structure.
- finemap_score
- ST2 statistical fine-mapping annotation score.
- TF
- ST2 predicted transcription-factor-binding annotation score.
- ABC
- ST2 activity-by-contact enhancer annotation score.
- ATAC
- ST2 ATAC-seq peak annotation score.
- CTCF
- ST2 CTCF ChIP-seq peak annotation score.
- Micro-C
- ST2 Micro-C contact annotation score for contact with a gene body or TSS.
- chromHMM
- ST2 ChromHMM chromatin-state annotation score.
- annotation_score
- ST2 sum of the integrative annotation scores.
- tier
- ST2 integrative variant tier (Tier1, Tier2 or Tier3).
- source_st4_row
- 1-based worksheet row in ST4 - MPRA variants.
- source_st2_row
- 1-based worksheet row in ST2 - Variant annotation; blank when the ST4 rsID has no matching ST2 row.
- source_note
- ST4 note describing cross-cell-line or cell-line-specific significance.
Quality control
Study QC required a perfect 230M library/probe match, excluded barcodes with read count <5, excluded barcodes lacking all four allele-specific probes (fwd_ref, fwd_alt, rev_ref and rev_alt), and excluded variant-replicate entries without matched DNA and RNA reads. Library-size correction used the upper quantile of nonzero counts; the scaled MPRAnalyze likelihood-ratio test included direction and replicate covariates. Post-filter median barcodes per variant were 322 in each HT29 replicate; median DNA/RNA read counts per variant were 41,970/10,670, 40,326/11,017 and 28,414/14,658 for replicates 1–3. All 275 rows in the released ST4 union result passed the package-level identifier/allele/numeric-value checks and were retained; rows not significant in HT29 were retained as informative negative results.
Curation notes
The processed table is derived from the public ST4 union table rather than controlled-access raw reads. The numeric ST4 FDR values yield 127 HT29 rows at FDR <1e-3, while the main text reports 133 HT29 significant variants; the source values were retained verbatim and the per-row significance indicator was computed from them. Ten ST4 rsIDs have no matching ST2 annotation row and therefore have blank coordinate/annotation fields; their MPRA results were retained. The EGA MPRA dataset EGAD50000000596 contains the raw sequencing files under access control and was not downloaded.