RegulomeDB statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

RegulomeDB specifications

Information


Unique identifier OMICS_30593
Name RegulomeDB
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.1
Maintained Yes

Maintainers


  • person_outline RegulomeDB
  • person_outline Michael Snyder

Publication for RegulomeDB

RegulomeDB citations

 (170)
library_books

Thirty loci identified for heart rate response to exercise and recovery implicate autonomic nervous system

2018
Nat Commun
PMCID: 5955978
PMID: 29769521
DOI: 10.1038/s41467-018-04148-1

[…] pipelines according to Schmitt et al. (40 kb resolution—correction applied to interactions with 50 kb-5 Mb span). We find the most significant promoter interactions for all potential regulatory SNPs (RegulomeDB score ≤5) in LD (r2 ≥ 0.8) with our sentinel SNPs and choose the interactors with the SNPs of highest regulatory potential to annotate the loci.We also performed enrichment testing across a […]

library_books

Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

2018
Nat Commun
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] Using the software HaploReg (version 4.1) and RegulomeDB v1.1, we investigated regulatory annotations for variants in LD (r2 > 0.8, 1000 genomes CEU) with the CCT-associated SNPs. To prioritize functional SNPs, we first used HaploRegv4.1 to extra […]

library_books

Family Based Genome Wide Association Study of South Indian Pedigrees Supports WNT7B as a Central Corneal Thickness Locus

2018
PMCID: 5961220
DOI: 10.1167/iovs.17-23536

[…] oadinstitute.org/mammals/haploreg/haploreg.php), respectively, that disrupts a Rad21 binding motif and a CTCF (CCCTC-binding factor) binding site, as well as other transcription factor binding sites (RegulomeDB, provided in the public domain, http://regulome.stanford.edu/; ) suggesting a role in regulation of gene expression. The region of intron 1 that includes the WNT7B SNPs associated with CCT […]

library_books

Biological Insights Into Muscular Strength: Genetic Findings in the UK Biobank

2018
Sci Rep
PMCID: 5915424
PMID: 29691431
DOI: 10.1038/s41598-018-24735-y

[…] R. We used OMIM database to search for known genetic disorders for mapped genes. In addition, we obtained CADD scores, the score of deleteriousness of SNPs predicted by 63 functional annotations, and RegulomeDB scores, representing regulatory functionality of SNPs based on eQTLs and chromatin marks. SNPs were also mapped with tissue-specific gene expression levels by utilizing GTEx database. We se […]

library_books

Integrative Bioinformatics Approaches for Identification of Drug Targets in Hypertension

2018
PMCID: 5894467
PMID: 29670885
DOI: 10.3389/fcvm.2018.00025

[…] res for each variant, among other information (). Although such integrative tools are useful for variant prioritization and interpretation, not all take into consideration tissue specificity aspects. RegulomeDB, for example, is a database that annotates SNPs with known and predicted regulatory elements in the intergenic regions of the human genome, calculating a score that reflects its evidence fo […]

library_books

A Comprehensive in Silico Analysis of Regulatory SNPs of Human CLEC7A Gene and Its Validation as Genotypic and Phenotypic Disease Marker in Recurrent Vulvovaginal Infections

2018
PMCID: 5869923
PMID: 29616193
DOI: 10.3389/fcimb.2018.00065

[…] nine SNPs including eight in 3′UTR region and one in intronic region were predicted to be affecting miRNA binding sites. In addition, one 3′UTR SNP rs12304716 was found to be affecting splicing also. RegulomeDB was further used to analyse these 26 cSNPs, which provided an annotation scores for 19 SNPs ranging from 4 to 6, representing weak or minimal binding evidence for the functional SNPs (Table […]

Citations

Looking to check out a full list of citations?

RegulomeDB institution(s)
Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
RegulomeDB funding source(s)
Supported by the ENCODE Consortium under Grant No. NIH 5U54 HG 004558 and by the Beta Cell Consortium under Grant No. VUMC 38204.

RegulomeDB reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review RegulomeDB