Regulatory Activity of Archaic Introgressed SNPs in Papuan Populations

25,869 high-confidence introgressed SNPs from Neanderthal and Denisovan lineages were tested for regulatory activity in immune cells. The dataset contains results from a massively parallel reporter assay, identifying 8.22% of Denisovan and 8.58% of Neanderthal sequences as active. It was created by Maddy Comerford and published on figshare in 2026.

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.
• Identify genes like IFIH1 and TNFAIP3 predicted to be regulated by differentially active archaic sequences.
• Examine the link between differential activity and differential transcription factor binding for introgressed variants.

Strengths

• Contains regulatory activity data for 25,869 specific introgressed SNPs.
• Experimental validation focuses on populations with high levels of Denisovan ancestry.
• Results quantify active regulatory activity for 8.22% of Denisovan and 8.58% of Neanderthal sequences tested.

Limitations

• The dataset is small in file size (46.6 KB), indicating limited scope and likely summary-level results rather than raw assay data.
• Sample data and column structure are unavailable, limiting understanding of the data's granularity.
• The dataset is derived from a specific study on Papuan genetic ancestry, which may limit generalizability to other populations.

Provenance

Source

figshare, authored by Maddy Comerford.

Collection Method

Data generated via a massively parallel reporter assay on introgressed SNPs in immune cell types.

Freshness

Last updated March 24, 2026.

Geography

Variants studied are segregating in present-day individuals of Papuan genetic ancestry.