An allele-focused MPRA tested paired alleles for 98 credible SNPs (196 total allele constructs) from the chromosome 8 autism-associated locus. HEK293T/17 cells were transfected in six biological replicate wells, and variant-level reporter activity was estimated from RNA barcode counts normalized to corresponding plasmid-DNA barcode counts.
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
CVCL:1926
Reference genome
GRCh38
Design focus
Variant-focused
Region of interest
chr8:38190000-38450000
Perturbation & assay details
Basal / Untreated
The library used 150-bp sequences centered on each candidate SNP, with paired alleles upstream of a minimal promoter/luc2 reporter and 20-bp random barcodes downstream of luc2. Six HEK293T/17 transfection wells were harvested 48 hours after transfection; aggregate RNA barcode counts were compared with plasmid-DNA barcode counts using the R mpra package/mpralm with normalization and replicate blocking. The paper calls the cells HEK293 but specifies ATCC CRL-11268, which corresponds to HEK293T/17.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (23 of 23)
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 · 23 definitions
variant_id
Variant rsID from Supplementary Table 13.
chromosome
Chromosome reported for the tested variant.
position_hg38
1-based variant position on hg38/GRCh38.
gwas_allele_1
GWAS A1 allele.
gwas_allele_2
GWAS A2 allele.
risk_allele
ASD risk allele reported in the supplementary MPRA results table.
odds_ratio_allele_1
GWAS odds ratio for A1.
gwas_p_value
GWAS association P-value reported for the locus variant.
reference_allele
MPRA reference allele (Ref) used in the allele contrast.
alternative_allele
MPRA alternative allele (Alt) used in the allele contrast.
published_logfc_alt_vs_ref
Published MPRA logFC estimate for Alt relative to Ref, preserved as supplied without a base transformation.
average_normalized_expression
Average normalized reporter expression used in the MPRA model.
t_statistic
Moderated t-statistic for the MPRA allele contrast.
mpra_p_value
Raw MPRA P-value for the Alt-versus-Ref contrast.
b_log_odds
B statistic, the log odds that the barcode is differentially expressed.
mpra_fdr
FDR-adjusted MPRA P-value (mpraFDR).
protective_allele
The tested allele opposite the reported risk allele, derived by matching risk to Ref or Alt.
logfc_risk_vs_protective
Effect-oriented logFC for risk allele relative to protective allele; sign is derived from the published Alt-versus-Ref estimate.
alt_vs_ref_effect_direction
Direction of reporter activity for Alt relative to Ref.
risk_vs_protective_effect_direction
Direction of reporter activity for the risk allele relative to the protective allele.
mpra_1_5fold_fdr_hit
TRUE when mpraFDR < 0.01 and absolute risk-versus-protective logFC exceeds ln(1.5), the 1.5-fold screen used for the reported candidate hits.
top_mpra_variant
TRUE for rs7001340, the strongest allelic MPRA result highlighted by the paper; FALSE otherwise.
qc_pass
TRUE for a complete row with a risk allele matching one of the tested Ref/Alt alleles and retained in the final published table.
Quality control
The authors performed barcode-coverage and biological-replicate reproducibility QC. Supplementary Figure 16 reports 6-596 barcodes per variant (mean 252.7449) across all 98 variants and approximately 0.99 correlation for the shown replicate comparisons. Their analysis removed barcode rows with four or more missing RNA replicate counts, unmapped barcode rows, and variants lacking both alleles. The published Supplementary Table 13 contains 98 complete variant rows and provides no row-level failure flag, so all 98 rows are retained after completeness and allele-pair validation. The derived mpra_1_5fold_fdr_hit flag uses FDR < 0.01 and absolute risk-versus-protective logFC > ln(1.5), matching the figure/code's 1.5-fold boundary.
Curation notes
The public supplementary source provides summarized variant-level MPRA statistics for all 98 tested SNPs, but no raw per-barcode DNA/RNA count matrices, barcode-to-allele mapping, or oligo sequence file was found in the cited public code repository or article data-availability statement. The processed table therefore preserves the complete published result rather than fabricating replicate-level counts. Allele strings were normalized to uppercase, including multi-base indel alleles. The supplementary table header describes logFC as a log2-fold-change, while the authors' plotting code and Figure 16 use a natural-log boundary corresponding to 1.5-fold; the published values are left unchanged and the derived screen is explicitly documented.