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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 citations

 (621)
call_split

Genetic variants of ALDH2 rs671 and CYP2E1 rs2031920 contributed to risk of hepatocellular carcinoma susceptibility in a Chinese population

2018
PMCID: 5942392
PMID: 29765251
DOI: 10.2147/CMAR.S162105
call_split See protocol

[…] nsu.ca/F-SNP/; accessed July 1, 2017) was used to mimic concrete mechanisms of the two SNP sites. Finally, the SNP function prediction website was employed to explore changes in the two SNPs (https://snpinfo.niehs.nih.gov/snpinfo/snpfunc.html, accessed July 1, 2017). […]

library_books

A catalog of potential putative functional variants in psoriasis genome wide association regions

2018
PLoS One
PMCID: 5929547
PMID: 29715312
DOI: 10.1371/journal.pone.0196635

[…] ing gene expression via various mechanisms, for example affecting TF binding affinity. We studied further SNP rs79824801 in the PFV set as an example. SNP rs79824801 is strongly linked with psoriasis tagSNP rs2066819 (LD r2 > 0.9 in both European and Eastern Asian populations in 1000 Genomes Project) on chromosome 12. It was simultaneously located in peaks of multiple histone marks, i.e. H3K27me3, […]

call_split

Genetic Insights Into Frailty: Association of 9p21 23 Locus With Frailty

2018
PMCID: 5938407
PMID: 29765957
DOI: 10.3389/fmed.2018.00105
call_split See protocol

[…] tory elements and target genes (). Functional Single Nucleotide Polymorphism; a web-based tool that integrates 16 databases and bioinformatic tools to uncover the functional effect of the SNPs () and FuncPred were used to predict the functional effects of associated variants. […]

library_books

Association of apolipoprotein E gene polymorphisms with blood lipids and their interaction with dietary factors

2018
PMCID: 5928585
PMID: 29712557
DOI: 10.1186/s12944-018-0744-2

[…] As shown in Table , of the seven tagSNPs at APOE, tagSNP rs445925 was significantly associated with total cholesterol (P = 0.003) after correction for multiple testing. The ‘A’ allele carriers (5.65 ± 0.98 mmol/L) had 5% lower levels of total cholest […]

library_books

RAN/RANBP2 polymorphisms and neuroblastoma risk in Chinese children: a three center case control study

2018
PMCID: 5940104
PMID: 29706609
DOI: 10.18632/aging.101429

[…] We chose potentially functional polymorphisms in the RAN/RANBP2 genes from dbSNP database (http://www.ncbi.nlm.nih.gov/). An online tool, SNPinfo (http://snpinfo.niehs.nih.gov/) was used to predict the functions of SNPs. In brief, we searched the potentially functional candidate SNPs located in the 5’- flanking region, 5’ untranslated r […]

call_split

Association of Raynaud’s phenomenon with a polymorphism in the NOS1 gene

2018
PLoS One
PMCID: 5919461
PMID: 29698501
DOI: 10.1371/journal.pone.0196279
call_split See protocol

[…] To minimise multiple testing, we chose tag SNPs accounting for most variation in the genes of interest. The LD TAG SNP Selection tool (https://snpinfo.niehs.nih.gov/snpinfo/snptag.html) was used to identify tagSNPs which were independent of one another (R2 < 0.65) using a European ancestral population (CEU), in all five candidate genes. A to […]

Citations

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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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