SNPinfo protocols

SNPinfo specifications

Information


Unique identifier OMICS_22324
Name SNPinfo
Software type Toolkit/Suite
Interface Web user interface
Restrictions to use None
Input data A list of candidate genes, a GWAS SNP list of Reference Sequence (rs) numbers with associated P-value from the GWAS of interest, or a list of linkage loci.
Database management system MySQL
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • FuncPred
  • GenePipe
  • GenomePipe
  • LinkagePipe
  • SNPseq
  • TagSNP

Maintainers


  • person_outline Zongli Xu <>
  • person_outline Jack Taylor <>

Additional information


https://snpinfo.niehs.nih.gov/snpinfo/guide.html

Publication for SNPinfo

SNPinfo IN pipelines

 (9)
2017
PMCID: 5509141
PMID: 28704393
DOI: 10.1371/journal.pone.0180046

[…] available exome sequencing project (e.g. charge, the nhlbi exome sequencing project). variants were annotated using annovar [37] and dbnsfp v2.0 according to grch37 and refseq. this multiple study snpinfo file was used as a component of the r package seqmeta (http://cran.rproject.org/web/packages/seqmeta/index.html)., we included age, sex, and apolipoprotein-e (apoe) as covariates […]

2016
PMCID: 5037665
PMID: 27589735
DOI: 10.3390/ijms17091385

[…] population tested with hapmap; (3) functional consequences; and (4) few or no studies on the role of the snp in mitral valve calcification. the national center for biotechnology information dbsnp, snpinfo, and snpnexus databases were utilized for the snp selection [20,21]. in total, we selected 50 snps within 24 genes (table 5)., the procedures of dna extraction and genotyping […]

2014
PMCID: 4047536
PMID: 24903211
DOI: 10.1038/srep05208

[…] (http://hapmap.ncbi.nlm.nih.gov/, hapmap data rel 24/phaseii nov08, on ncbi b36 assembly, dbsnp b126), chb. second, we placed the position of each gene into an integrated bioinformatics tool “snpinfo”43 (http://snpinfo.niehs.nih.gov/snpinfo/snpfunc.htm) and retrieved a set of snps with possible functions. third, we filtered these snps by maf of chb >10%, and got a total of 52 snps […]

2014
PMCID: 4047536
PMID: 24903211
DOI: 10.1038/srep05208

[…] hapmap data rel 24/phaseii nov08, on ncbi b36 assembly, dbsnp b126), chb. second, we placed the position of each gene into an integrated bioinformatics tool “snpinfo”43 (http://snpinfo.niehs.nih.gov/snpinfo/snpfunc.htm) and retrieved a set of snps with possible functions. third, we filtered these snps by maf of chb >10%, and got a total of 52 snps in the 7 candidate […]

2014
PMCID: 4047536
PMID: 24903211
DOI: 10.1038/srep05208

[…] hapmap data rel 24/phaseii nov08, on ncbi b36 assembly, dbsnp b126), chb. second, we placed the position of each gene into an integrated bioinformatics tool “snpinfo”43 (http://snpinfo.niehs.nih.gov/snpinfo/snpfunc.htm) and retrieved a set of snps with possible functions. third, we filtered these snps by maf of chb >10%, and got a total of 52 snps in the 7 candidate genes. as shown […]

SNPinfo institution(s)
Epidemiology Branch National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
SNPinfo funding source(s)
Supported by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences.

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