#DHS-Mining# dhs-mining gives epigenetic information for SNPs-eQTL pairs from CoDeS3D.
The dhs.db (created by init_dhsDB.py) includes the following tables from the Regulatory Elements DB (Sheffield et al, 2013):
- Gene Correlations (of known genes with DHSs, p values <= 0.05)
- Overlap (of DHS, CpG sites and promoters)
- Concordance (cell lines, types and tissues of the ENCODE samples in the database)
- Open Cell Types (DHS clusters with the samples, cell types and tissues in which they are found)
- DHS Predictors (coordinates of DHSs, their clusters and tissues)
- Open Samples (DHS clusters; counts of DHS, open samples; samples, tissues with max counts)
- Motif (assigned to transcription factors based on the JASPAR database)
- DHS (coordinates of DHSs and their raw signals)
- Gene Expression (data of the 112 samples used in the study)