rSNPBase protocols

View rSNPBase computational protocol

rSNPBase statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Regulatory variant prediction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

rSNPBase specifications

Information


Unique identifier OMICS_28870
Name rSNPBase
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.1
Stability Stable
Maintained Yes

Maintainers


  • person_outline Jing Wang <>
  • person_outline Liyuan Guo <>

Publications for rSNPBase

rSNPBase in pipelines

 (4)
2018
PMCID: 5940861
PMID: 29740051
DOI: 10.1038/s41598-018-25553-y

[…] location, genomic and phylogenetic context of rs6918289 were determined on the human genome (grch38.p10) using ensembl browser. the putative regulatory role of rs6918289 was established using rsnpbase, and the phylop score was obtained using phylop software., extensive data is provided with this article and further information is available from the authors on request., , vesna gorenjak […]

2017
PMCID: 5330487
PMID: 28245265
DOI: 10.1371/journal.pone.0172880

[…] ranked variants until their cumulative posterior probability exceeds 0.99., the variants identified during fine mapping were annotated using a variety of tools, including haploreg, regulomedb and rsnpbase., the program eigensoft [] was used to perform a principal components analysis, after pruning markers showing short-range and long-range linkage disequilibrium using a threshold of r2 = […]

2017
PMCID: 5635123
PMID: 29018269
DOI: 10.1038/s41598-017-12885-4

[…] to the f-snp database, rs2229857 seems to alter a putative exonic splicing enhancer (ese). functional analysis of rs2229857, rs1127313, rs1127314, rs1127317 and rs1127326 polymorphisms by using rsnpbase reported that each of them could be involved in transcriptional regulation. additionally, rs1127313 and rs1127314 are 3′utr variants and seem to be involved in the mirna binding site […]

2014
PMCID: 4152274
PMID: 25180498
DOI: 10.1371/journal.pone.0106442

[…] cell lines , (). the 3′utr of havcr2 is moderately conserved in mammals, as assessed through the gerp (genomic evolutionary rate profiling) score (); prediction of regulatory motifs using rsnpbase indicated that rs4704846 maps to regions showing h3k27ac histone marks (usually associated with active regulatory elements) in cd14+ monocytes and several microrna binding sites […]


To access a full list of citations, you will need to upgrade to our premium service.

rSNPBase in publications

 (12)
PMCID: 5940861
PMID: 29740051
DOI: 10.1038/s41598-018-25553-y

[…] also, our bioinformatic analyses indicate that rs6918289 is located in a transcriptional region of adc10p1 gene that could impact trem2 transcription levels. indeed, rs6918289 is referred by rsnpbase (http://rsnp.psych.ac.cn/) as a post-transcriptional regulatory element and, in lymphocyte b cells, rs6918289 is associated with the pabpc1 protein. the pabpc1 protein binds to the 3′ […]

PMCID: 5816861
PMID: 29484037
DOI: 10.1155/2018/5812802

[…] evaluated by the snp function prediction tool [] using the transfac database on potential transcription factor recognition sites (biobase corporation, wolfenbuettel, germany) as well as by using the rsnpbase database of curated regulatory snps (http://rsnp.psych.ac.cn) []., the genotype and allele frequencies of cyp4a11 and cyp4f2 snps are shown in . a significant departure from hardy–weinberg […]

PMCID: 5635123
PMID: 29018269
DOI: 10.1038/s41598-017-12885-4

[…] the functional effects of snps obtained from 16 bioinformatics tools and databases b) ensembl’s variant effect predictor (vep) tool (http://grch37.ensembl.org/info/docs/tools/vep/index.html) c) rsnpbase (http://rsnp.psych.ac.cn/) that provides regulatory annotations on rsnps; and d) mirdb target prediction (http://mirdb.org/mirdb/index.html) for identification of mirna target sequences,., […]

PMCID: 5330487
PMID: 28245265
DOI: 10.1371/journal.pone.0172880

[…] role. annotation on haploreg v4.1 also indicates that this polymorphism is an eqtl, alters fiver regulatory motifs, and overlaps with an enhancer in fat, liver and blood. finally, the database rsnpbase also indicates that rs964184 may be involved in proximal transcriptional regulation., here, we present the results of an admixture mapping analysis of lipid traits in two independent samples […]

PMCID: 5269754
PMID: 28128292
DOI: 10.1038/srep41399

[…] the haploreg v4.1 database (http://www.broadinstitute.org/mammals/haploreg/haploreg.php), forming the candidate snps. the potential functional consequences of the candidate snps were predicted using rsnpbase (http://rsnp.psych.ac.cn/) and regulomedb databases (http://www.regulomedb.org/). the rsnpbase database provides the regulatory information on snps with experimentally validated regulatory […]


To access a full list of publications, you will need to upgrade to our premium service.

rSNPBase institution(s)
CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China; Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
rSNPBase funding source(s)
Supported by CAS Key Laboratory of Mental Health, Institute of Psychology; CAS/SAFEA International Partnership Program for Creative Research Teams [Y2CX131003]; Knowledge Innovation Program of the Chinese Academy of Sciences [KSCX2-EW-J-8]; National Natural Science Foundation of China [81201046].

rSNPBase reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review rSNPBase