SNPinfo pipeline

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


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

Maintainers


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

Additional information


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

Publication for SNPinfo

SNPinfo citations

 (5)
2018
PMCID: 5813178

[…] genotypes with tooth agenesis adjusted for family history of cancer and gender., annotation of the newly identified loci was performed using the dbnsfp24 and funcpred (https://snpinfo.niehs.nih.gov/snpinfo/snpfunc.html) databases. information on the function of the associated snps regarding splicing regulation, stop codon, polyphen predictions, transcription factor binding site predictions, […]

2015
PMCID: 4423106

[…] concentration and quality were measured using nanodrop┬« nd-1000 (nanodrop technologies, wilmington, de, usa)., snps in the tfpi and tf gene regions were selected using a snp tagging approach. the tagsnp selection was performed using the tagger program [35] implemented in haploview v. 4.2. and genotype data from the caucasian population (utah residents with ancestry from northern and western […]

2014
PMCID: 4047536

[…] of 52 snps in the 7 candidate genes. as shown in supplementary table s3 online, the detailed information of all the snps were listed, including the possible functions of allelic difference which the snpinfo tool can predict (marked with a y letter), such as tfbs, splicing site, microrna-binding site, nonsynonymous snp, polymorphism phenotyping. forth, we tested the ld among these snps […]

2013
PMCID: 3617303

[…] markers with minor allele frequency (maf) greater than 1% in the japanese population (rs3821949, rs12532, and rs4464513) were selected using the web-based program tag snp selection (tagsnp; http://snpinfo.niehs.nih.gov/guide.htm#snptag) (21)., these snps achieved high "design scores" (a predictor of usable genotypes provided by illumina inc., san diego, ca, usa). their heterozygosity […]

2011
PMCID: 3203108

[…] algorithm to infer genotypes for individuals. we identified an approximately 2 mb region on chromosome 12 (45553633 to 47551615 bp) which included vdr. since many of the markers typed in our tagsnp set were missing in the phased haplotypes of the hapmap data phase iii/rel#3 (may10), we downloaded the most recent snp genotype data (hapmap data rel#28 phase ii and iii) for both the yri […]

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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