SNPper protocols

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SNPper specifications

Information


Unique identifier OMICS_01926
Name SNPper
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No

Taxon


  • Primates
    • Homo sapiens

Maintainer


This tool is not available anymore.

Publication for SNPper

SNPper in pipelines

 (3)
2010
PMCID: 2815792
PMID: 20140262
DOI: 10.1371/journal.pone.0009040

[…] tests. stata version 10 statistical software was used for all analyses (statacorp, college station, tx)., gene names, marker positions (base pair – bp) and marker function were identified using the snpper database (http://snpper.chip.org). allele and genotype differences between cases and controls, deviations in hardy-weinberg equilibrium (hwe) and inbreeding coefficients (f) were calculated […]

2009
PMCID: 2762536
PMID: 19434427
DOI: 10.1007/s00439-009-0677-y

[…] ) both store known snps, but specifically attempt to associate them with known transcription factor-binding sites for identification of potential regulatory snps. mapper is a companion tool to the snpper retrieval system and database that locates computationally predicted transcription factor-binding sites (riva and kohane ). both polymapr (freimuth et al. ) and pupasnp finder (conde et al. ) […]

2006
PMCID: 1508148
PMID: 16600026
DOI: 10.1186/1465-9921-7-60

[…] was obtained from dbsnp [], innate immunity pga [] and ucsc genome browser []. snp selection was done with the help of perlegen [] and hapmap [] data. sequence context annotation was done by snpper [], pupa [], tamal [] and snppi [])., the total sample consisted of 947 individuals from 224 families where 872 serum measurements of 25-oh-d3, 876 1,25- oh2-d3 and 934 total ige measurements […]


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SNPper in publications

 (52)
PMCID: 5342796
PMID: 27738313
DOI: 10.18632/oncotarget.12582

[…] cells (figure ). similarly, increased sox17 expression decreased maml3 mrna and protein levels (figure )., multi-genome analysis of positions and patterns of elements of regulation (mapper, http://snpper.chip.org/mapper/mapper-main) identified a putative sox17 binding site located −803 to −809 bp from the transcription start site in the maml3 promoter region (figure ). a chromatin […]

PMCID: 5029869
PMID: 27648838
DOI: 10.1371/journal.pone.0163170

[…] snps was based mainly on literature search, as a way to replicate previous associations. we have also searched for additional snps in coding and regulatory regions of all candidate genes using the snpper tool. in order to increase gene coverage, tag snps were selected from hapmap data bank using the following parameters: minor allele frequency of 0.05 in ceu (utah residents with northern […]

PMCID: 5173039
PMID: 27191502
DOI: 10.18632/oncotarget.9351

[…] this variant was not identified using melacarta software in south island patients, and it has not been previously reported as a polymorphic variant in four snp databases (dbsnp/uniprot, snpper, alfred, or snpedia). interestingly, the ephb6g404s mutation occurred significantly more frequently in melanomas without detectable braf or nras mutations., overall, nras mutations […]

PMCID: 4832550
PMID: 27080863
DOI: 10.1186/s12863-016-0367-4

[…] quantitative polymerase chain reaction (qpcr) (thermo scientific, pittsburgh pa, usa) in a 20 μl reaction., we used the online tools snap for identifying proxy snps for the ms associated snps [] and snpper [] for determining which of these proxies were transcribed for all 110 non-hla ms-associated snps recently reported [, ]. three genes, which had a transcribed ms-associated snp or transcribed […]

PMCID: 4783434
PMID: 26765264
DOI: 10.1038/gene.2015.61

[…] a/g g g/t t c a n n n a/g g g/t t c a (bold labels the nucleotides that deviates from the consensus sequence), the identity of the ms-associated snps,, the location of the ms-associated snps http://snpper.chip.org/, and gene expression data from http://biogps.org of the indicated genes compared with mean value of gene expression in all tissues/cells tested in brackets., snps […]


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SNPper institution(s)
Children's Hospital Informatics Program, Children's Hospital, Harvard Medical School, Boston, MA, USA
SNPper funding source(s)
Supported by grant U01-HL66795 from the National Heart, Lung and Blood Institute of NIH.

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