Large T2D-linked variant library across INS/SCP1 promoter and fragment-position contexts

Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions

The first MPRA screened 198-bp fragments centered on or offset around variants linked to type 2 diabetes and related metabolic traits in INS-1 832/13 rat insulinoma cells. The processed table summarizes 11,656 fragments represented across all four plasmid contexts: upstream or downstream of the human INS or synthetic SCP1 promoter.

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: NCBITaxon:10116
Taxonomy ID: NCBITaxon:10116
Biosample: CVCL:7226
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

No exogenous treatment; transient electroporation and 24-hour reporter expression

Modified STARR-seq-derived episomal reporter with 16-bp random barcodes. The four configurations combined the 408-bp human INS promoter or 81-bp SCP1 promoter with a fragment cloned upstream or downstream of the promoter/reporter cassette; RNA barcode counts were normalized to plasmid-input DNA barcode counts. The library was electroporated into INS-1 832/13 cells, with three biological replicates per configuration. The paper used MPRAnalyze for per-fragment activity and joint promoter/position contrasts.

Processed data

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Visible columns (68 of 68)

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Column dictionary · 68 definitions

fragment_id: Unique author/library fragment identifier.
rsid: Variant identifier from the author fragment name; composite coordinate/allele IDs are retained when no dbSNP rsID was available.
chromosome: Chromosome of the 198-bp fragment in hg19.
start_hg19: 0-based hg19 start coordinate of the tested fragment.
end_hg19: hg19 end coordinate of the tested fragment.
reference_allele: Reference allele at the focal variant.
alternate_allele: Alternate allele at the focal variant.
fragment_allele: Allele carried by this oligo, reference or alternate.
variant_position_context: Location of the focal variant within the fragment: snpleft, snpctr, or snpright.
library_subset: Author annotation class: enh, pro, or oth.
trait: Trait or trait combination associated with the proxy variant in the library annotation.
index_rsid: Index GWAS signal identifier or source index coordinate from the author annotation.
ld_r2: Linkage-disequilibrium R-squared between the tested proxy and index signal.
sequence_198bp: 198-bp genomic sequence used as the regulatory fragment.
sequence_230bp_with_adapters: Full synthesized 230-bp oligo sequence including cloning adapters.
annotation_match: Whether the fragment was matched to a GSE279057 library annotation.
alpha_natural_log_ins_upstream: Author MPRAnalyze alpha activity estimate on the natural-log scale for INS upstream.
activity_log2_ins_upstream: Author Alpha_corrected activity score on the base-2 log scale for INS upstream.
zscore_ins_upstream: Author MPRAnalyze Z-score activity statistic for INS upstream.
zscore_pvalue_ins_upstream: Nominal author Z-score p-value for INS-upstream activity.
zscore_qvalue_ins_upstream: Package Benjamini-Hochberg q-value for the full INS-upstream author result set using Z-score p-values.
mad_statistic_ins_upstream: Author median-absolute-deviation activity statistic for INS upstream.
mad_pvalue_ins_upstream: Nominal author MAD-based p-value for INS-upstream activity.
mad_qvalue_ins_upstream: Package Benjamini-Hochberg q-value for the full INS-upstream author result set using MAD p-values.
active_fdr05_zscore_ins_upstream: Whether the package Z-score q-value is at most 0.05 for INS upstream.
active_fdr05_mad_ins_upstream: Whether the package MAD q-value is at most 0.05 for INS upstream.
alpha_natural_log_ins_downstream: Author MPRAnalyze alpha activity estimate on the natural-log scale for INS downstream.
activity_log2_ins_downstream: Author Alpha_corrected activity score on the base-2 log scale for INS downstream.
zscore_ins_downstream: Author MPRAnalyze Z-score activity statistic for INS downstream.
zscore_pvalue_ins_downstream: Nominal author Z-score p-value for INS-downstream activity.
zscore_qvalue_ins_downstream: Package Benjamini-Hochberg q-value for the full INS-downstream author result set using Z-score p-values.
mad_statistic_ins_downstream: Author median-absolute-deviation activity statistic for INS downstream.
mad_pvalue_ins_downstream: Nominal author MAD-based p-value for INS-downstream activity.
mad_qvalue_ins_downstream: Package Benjamini-Hochberg q-value for the full INS-downstream author result set using MAD p-values.
active_fdr05_zscore_ins_downstream: Whether the package Z-score q-value is at most 0.05 for INS downstream.
active_fdr05_mad_ins_downstream: Whether the package MAD q-value is at most 0.05 for INS downstream.
alpha_natural_log_scp1_upstream: Author MPRAnalyze alpha activity estimate on the natural-log scale for SCP1 upstream.
activity_log2_scp1_upstream: Author Alpha_corrected activity score on the base-2 log scale for SCP1 upstream.
zscore_scp1_upstream: Author MPRAnalyze Z-score activity statistic for SCP1 upstream.
zscore_pvalue_scp1_upstream: Nominal author Z-score p-value for SCP1-upstream activity.
zscore_qvalue_scp1_upstream: Package Benjamini-Hochberg q-value for the full SCP1-upstream author result set using Z-score p-values.
mad_statistic_scp1_upstream: Author median-absolute-deviation activity statistic for SCP1 upstream.
mad_pvalue_scp1_upstream: Nominal author MAD-based p-value for SCP1-upstream activity.
mad_qvalue_scp1_upstream: Package Benjamini-Hochberg q-value for the full SCP1-upstream author result set using MAD p-values.
active_fdr05_zscore_scp1_upstream: Whether the package Z-score q-value is at most 0.05 for SCP1 upstream.
active_fdr05_mad_scp1_upstream: Whether the package MAD q-value is at most 0.05 for SCP1 upstream.
alpha_natural_log_scp1_downstream: Author MPRAnalyze alpha activity estimate on the natural-log scale for SCP1 downstream.
activity_log2_scp1_downstream: Author Alpha_corrected activity score on the base-2 log scale for SCP1 downstream.
zscore_scp1_downstream: Author MPRAnalyze Z-score activity statistic for SCP1 downstream.
zscore_pvalue_scp1_downstream: Nominal author Z-score p-value for SCP1-downstream activity.
zscore_qvalue_scp1_downstream: Package Benjamini-Hochberg q-value for the full SCP1-downstream author result set using Z-score p-values.
mad_statistic_scp1_downstream: Author median-absolute-deviation activity statistic for SCP1 downstream.
mad_pvalue_scp1_downstream: Nominal author MAD-based p-value for SCP1-downstream activity.
mad_qvalue_scp1_downstream: Package Benjamini-Hochberg q-value for the full SCP1-downstream author result set using MAD p-values.
active_fdr05_zscore_scp1_downstream: Whether the package Z-score q-value is at most 0.05 for SCP1 downstream.
active_fdr05_mad_scp1_downstream: Whether the package MAD q-value is at most 0.05 for SCP1 downstream.
ins_minus_scp1_log2_activity_upstream: INS-upstream activity_log2 minus SCP1-upstream activity_log2.
ins_minus_scp1_log2_activity_downstream: INS-downstream activity_log2 minus SCP1-downstream activity_log2.
upstream_minus_downstream_log2_activity_ins: INS-upstream activity_log2 minus INS-downstream activity_log2.
upstream_minus_downstream_log2_activity_scp1: SCP1-upstream activity_log2 minus SCP1-downstream activity_log2.
author_promoter_bias_log2_fold_change: Author joint MPRAnalyze log2 fold-change for the promoter contrast; contrast orientation follows Table S9.
author_promoter_bias_statistic: Author Wald statistic for promoter bias from Table S9.
author_promoter_bias_pvalue: Author Wald-test p-value for promoter bias from Table S9.
author_promoter_bias_fdr: Author FDR for promoter bias from Table S9.
author_position_bias_log2_fold_change: Author joint MPRAnalyze log2 fold-change for the position contrast; contrast orientation follows Table S10.
author_position_bias_statistic: Author Wald statistic for position bias from Table S10.
author_position_bias_pvalue: Author Wald-test p-value for position bias from Table S10.
author_position_bias_fdr: Author FDR for position bias from Table S10.

Quality control

Author QC excluded non-SNV designs at library construction, filtered barcode-fragment associations by mapping quality/sequencing depth and removed duplicate barcodes, then restricted the common-fragment analysis to elements represented by more than two barcodes and at least 10 input DNA counts in all four configurations. The package additionally retained only finite author activity and joint-bias statistics present in all four S4-S7 tables and S9-S10, with a matching GSE279057 annotation: 11,656 of 11,656 common fragments passed. Context q-values are package-computed Benjamini-Hochberg adjustments of the full-table Z-score and MAD p-values; author S9/S10 FDR values are preserved separately.

Curation notes

The table is a wide fragment-level join of publisher Tables S4-S7 (four construct contexts), S9 (promoter bias), S10 (position bias), and the GSE279057 annotation file. It intentionally retains both reference and alternate oligos even though the paper states that the first library did not have enough pairing complexity for sensitive allelic-effect analysis. The source annotation uses hg19 coordinates; package-computed q-values are clearly distinguished from author-provided FDR values.

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