SNPinfo protocols

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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

 (10)
2017
PMCID: 5509141
PMID: 28704393
DOI: 10.1371/journal.pone.0180046

[…] one available exome sequencing project (e.g. charge, the nhlbi exome sequencing project). variants were annotated using annovar [] 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 […]

2017
PMCID: 5571531
PMID: 28244652
DOI: 10.1111/jcmm.13093

[…] six tag snps in lep and 26 tag snps in lepr were selected for further evaluation. we used the bioinformatics tools f‐snp (http://com pbio.cs.queensu.ca/f‐snp/) and snp function prediction (http://snpinfo.niehs.nih.gov/snpinfo/snpfunc.htm) to assess the predicted functional effects of each tag snp , . the test for functional snp aimed to evaluate the potentially deleterious functional impact […]

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 [,]. in total, we selected 50 snps within 24 genes ()., the procedures of dna extraction and genotyping were the same as previously […]

2016
PMCID: 5117545
PMID: 27871331
DOI: 10.1186/s13052-016-0311-2

[…] b126) to search for snps localized within gene regions with maf ≥ 0.05 in the chinese han population. subsequently, a web-based analysis tool was used to predict the function of these snps (https://snpinfo.niehs.nih.gov/snpinfo/snpfunc.php). finally, a total of 8 potentially functional snps were selected. we next conducted linkage disequilibrium (ld) analysis using haploview 4.2 software (broad […]

2016
PMCID: 5166553
PMID: 27994680
DOI: 10.7150/jca.16507

[…] gene polymorphisms with susceptibility to ptc in a han chinese population., a total of 861 patients with ptc, 562 disease controls with nodular goiter and 897 healthy controls were recruited. four tagsnp polymorphisms (rs12427141, rs712, rs7315339 and rs7960917) of kras gene were genotyped by matrix-assisted laser desorption/ionization time of flight mass spectrometry (maldi-tof-ms). […]


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SNPinfo in publications

 (533)
PMCID: 5942392
PMID: 29765251
DOI: 10.2147/CMAR.S162105

[…] 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)., the hardy–weinberg equilibrium was calculated by the goodness-of-fit χ2 test. the χ2 test was performed to analyze the association […]

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

[…] 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. […]

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

[…] in either cohort. in the precise study, after correction for multiple testing, there was a statistically significant association of the apoe haplotype (rs7412 and rs429358; e2, e3, and e4) and apoe tagsnp rs445925 with total cholesterol (p = 4 × 10− 4 and p = 0.003, respectively). carriers of the e2 allele had lower total cholesterol concentration (5.54 ± 0.97 mmol/l) than those with the e3 […]

PMCID: 5919461
PMID: 29698501
DOI: 10.1371/journal.pone.0196279

[…] responses from questionnaires to diagnose rp [, ]., 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. […]

PMCID: 5905129
PMID: 29692895
DOI: 10.1186/s40170-018-0177-4

[…] used the penncnv software (parameters: exome hmm model with gcmodel adjustment, filtered by 10 snps minimum 10 and with region length longer than 50 k) [], the r package genocn (parameters: cnv-only snpinfo$pfb > 1; outputsnp 1; outputseg true) [], and the r package rawcopy (default parameters) [] for cnv inference. cnv calls were obtained by integrating the output from all callers., rna […]


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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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