SNAP protocols

SNAP specifications


Unique identifier OMICS_01927
Alternative name SNP Annotation and Proxy Search
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No


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Publication for SNP Annotation and Proxy Search

SNAP IN pipelines

PMCID: 4051592
PMID: 24514566
DOI: 10.1038/mp.2013.197

[…] genotyped snps and snps selected from our differential gene expression analyses. the genome-wide complex trait analysis was fitted using a restricted maximum likelihood method. the broad institute's snap online plotting tool28 was used to generate the regional association and recombination rate plots., the same conditions were used when investigating the association between rs7171755 and iq […]

PMCID: 4055950
PMID: 24920014
DOI: 10.1038/ncomms4856

[…] sas version 9.2 (sas institute inc., cary, nc, usa) and r15.1 (r project). locuszoom51 was used for regional visualization of results. ld statistics were calculated based on hapmap3 release 2 using snap proxy search52. in each of the three discovery gwas analyses, quality control included removal of individuals with cryptic relatedness and a genotyping call rate of <0.95. additionally, snps […]

PMCID: 3561129
PMID: 23382694
DOI: 10.1371/journal.pgen.1003240

[…] best associated haplotypic configuration were checked for availability in ghs. if a given htsnp was not genotyped in ghs, we sought whether we could find a genotyped proxy snp (r2>0.80) using the snap software [18]. replication in ghs of the haplotypic signals observed in cts was assessed using the thesias software [21] implementing the same statistical haplotype model as in the gridhaplo […]

PMCID: 2794362
PMID: 20072603
DOI: 10.1371/journal.pgen.1000806

[…] program [32] was utilized to impute the genotypes of all snps located in the regions based on asian hapmap data. snptest [32] was used to test for associations between the imputed snps and of. snap was used to depict the regional association plot [33]., we thank the framingham heart study and the framingham share project, which are conducted and supported by the national heart, lung, […]

SNAP institution(s)
The Framingham Heart Study of the National Heart, Lung, and Blood Institute of the National Institutes of Health and Boston University School of Medicine, Framingham, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School-Partners HealthCare Center for Genetics and Genomics, Boston, MA; Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
SNAP funding source(s)
Supported by NHLBI's Framingham Heart Study (N01-HC-25195); Intramural training program of the NHLBI; and a NHLBI CARe (Candidate Gene Association Resource) grant (N01-HC-65226).

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