14q24 allele-specific MPRA screen
Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locusA plasmid-based MPRA tested 39 linkage-disequilibrium-linked candidate SNPs in the 14q24 renal cell carcinoma susceptibility locus, with alternative alleles represented by barcoded forward and reverse constructs. Reporter RNA/DNA signals were modeled jointly across ACHN and HEK293T cells under normoxia and 1% oxygen hypoxia.
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 transfection; oxygen condition varied between normoxia and 1% O2 hypoxia
The library was part of a larger 774-variant screen and included 39 variants from 14q24. For each allele, ten forward and ten reverse oligos with unique random 10-bp barcodes were synthesized; scrambled sequences served as controls. The reporter library was transfected with Lipofectamine 3000 into ACHN renal cancer cells and HEK293T embryonic kidney cells, with normoxic and 1% O2 hypoxic conditions. Poly(A)-enriched reporter RNA and plasmid DNA barcode/vector reads were sequenced on an Illumina HiSeq 2500, and SNP-level effects were estimated by logistic regression including allele, oligo direction, cell type, and condition.
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 · 24 definitions
- variant_id
- dbSNP identifier for the tested variant.
- chromosome
- Chromosome number from the source supplemental table.
- position_hg19
- Variant coordinate on the hg19/GRCh37 assembly.
- position_grch38
- Variant coordinate on the GRCh38/hg38 assembly supplied by the source.
- region
- RCC susceptibility region label supplied by the source.
- tested_alleles
- Alleles listed by the source for the tested SNP, separated by slashes.
- minor_allele
- Minor allele annotation supplied by the source table.
- minor_allele_frequency
- Minor allele frequency supplied by the source table.
- n_alleles_assayed
- Number of alleles reported as assayed by the source.
- alternative_allele
- Allele encoded as the alternative allele in the source regression model.
- allelic_pvalue
- Source pAllele: p value for the allele-specific MPRA effect in the model including direction, cell type, and condition.
- allelic_qvalue_bonferroni_774
- Source qAllele: Bonferroni-corrected allele-effect p value across 774 tested variants.
- allelic_beta
- Source bAllele: regression coefficient for the allele-specific effect, with sign as reported for the alternative-allele model coding.
- variance_explained
- Source Var_exp: estimated fraction of MPRA signal variance explained by the allele-specific effect.
- direction_pvalue
- Source pDirection: p value for forward versus reverse oligo-direction effect.
- direction_beta
- Source bDirection: beta coefficient for oligo-direction effect.
- cell_type_pvalue
- Source pCellType: p value for ACHN versus HEK293T cell-type effect.
- cell_type_beta
- Source bCellType: beta coefficient for cell-type effect.
- condition_pvalue
- Source pCondition: p value for normoxia versus hypoxia condition effect.
- condition_beta
- Source bCondition: beta coefficient for oxygen-condition effect.
- alternative_allele_effect
- Interpretation of the sign of allelic_beta: higher or lower reporter activity for the modeled alternative allele.
- allelic_qvalue_pass
- True when the source Bonferroni-corrected allelic q value is below 0.05.
- minor_allele_consistent_with_tested_alleles
- True when the source minor-allele annotation appears in the source tested-alleles string; False flags a source metadata mismatch.
- qc_pass
- Package-level QC result; all retained rows have complete required fields, finite numeric values, valid probability/MAF ranges, and an alternative allele present in tested_alleles.
Quality control
The authors confirmed transfection efficiency above 70% with a parallel GFP transfection, checked DNase treatment by PCR with no DNA contamination detected, mapped barcode and vector sequences from paired-end reads, normalized barcode counts per 1,000,000 reads, normalized each barcode to the median of its scramble controls, and corrected SNP-level p values by Bonferroni over 774 comparisons. The processed table retains the 39 14q24 variants reported in Supplemental Table S2 because all have complete required coordinates and model statistics and pass finite-value, probability/range, and alternative-allele consistency checks. Four source minor-allele annotations do not occur in their listed tested-allele strings; these rows are retained because the MPRA effect fields are complete and the mismatch is explicitly flagged in the table.
Curation notes
This is one combined MPRA experiment because the available Table S2 reports one SNP-level regression across both ACHN and HEK293T cells, both oligo directions, and normoxia/hypoxia rather than separate stratum-level activity tables. The paper's lead result is rs4903064: the C risk allele has higher reporter expression than T in both orientations, and the source bAllele is negative because T is the modeled alternative allele. Cellosaurus identifiers are CVCL:1067 for ACHN and CVCL:0063 for HEK293T; biosample_id lists both because the experiment used both lines. The source table contains four minor-allele annotation mismatches, which are preserved and flagged rather than corrected.