Massively Parallel Reporter Assay Data on Archaic Human Introgressed SNPs

Massively parallel reporter assay data contains regulatory activity measurements for 25,869 high-confidence introgressed SNPs from Neanderthal and Denisovan lineages. The dataset, created by Maddy Comerford, experimentally validates how these archaic variants influence gene regulation in immune cell types from individuals of Papuan genetic ancestry.

Use Cases

• Analyze the association between introgressed allele frequency and regulatory activity for Denisovan and Neanderthal sequences.
• Investigate the relationship between differential regulatory activity and distance to the nearest transcription start site.
• Predict immune-related genes like IFIH1 and TNFAIP3 regulated by differentially active archaic sequences.
• Examine the link between differential activity and evidence of differential transcription factor binding.

Strengths

• Contains 25,869 high-confidence introgressed SNPs for analysis.
• Provides experimental validation of regulatory activity for archaic variants in a key population.
• Data is structured in an XLSX file format, facilitating tabular analysis.
• Released under a permissive CC BY 4.0 license.

Limitations

• The dataset is relatively small at 5.1 MB, potentially limiting the scope for certain large-scale analyses.
• The specific row count and column structure are unknown, complicating initial data assessment.
• Focus is exclusively on individuals of Papuan genetic ancestry, limiting generalizability to other populations.

Provenance

Source

Maddy Comerford via figshare.

Collection Method

Data generated using a massively parallel reporter assay (MPRA).

Freshness

Last updated March 24, 2026.

Geography

Derived from individuals of Papuan genetic ancestry.