SNPsea protocols

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SNPsea statistics

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Associated diseases

Associated diseases

SNPsea specifications


Unique identifier OMICS_18197
Name SNPsea
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of SNP identifiers and a matrix of genes and conditions.
Input format TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.3
Stability Stable
Source code URL
Maintained Yes



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  • person_outline Soumya Raychaudhuri <>

Publication for SNPsea

SNPsea in pipeline

PMCID: 4767573
PMID: 26808113
DOI: 10.1038/ng.3496

[…] enrichr:, geneatlas:, immgen,, fantom5:, snpsea:, r version 3.0.0:, proc:, haplotter:, hgdp selection browser: […]

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SNPsea in publications

PMCID: 5852557
PMID: 29370075
DOI: 10.3390/genes9020061

[…] database is a powerful resource where the link between gene and the tissue that is affected is investigated []. similarly, for many ocular traits, an ocular tissues database has been utilized []. snpsea is a tool developed at the broad institute (cambridge, ma, usa) to help prioritize the genetic associations to identify tissues and pathways that are affected by the expression of specific […]

PMCID: 5192301
PMID: 28070503
DOI: 10.1155/2016/7983236

[…] is to determine which pathways are affected by these mutations. common pathway resources and tools used for these types of analysis include kegg [], david [], string [], berex [], dapple [], and snpsea []., kegg represents one of the most popular databases for pathway analysis. david is a popular online tool for performing functional enrichment analysis based on user defined gene lists. […]

PMCID: 4889647
PMID: 27172182
DOI: 10.1534/g3.116.027326

[…] we aimed to elucidate the cell types, tissues, and pathways influenced by common variants in systemic lupus erythematosus (sle). we applied a nonparameter enrichment statistical approach, termed snpsea, in 181 single nucleotide polymorphisms (snps) that have been identified to be associated with the risk of sle through genome-wide association studies (gwas) in eastern asian and caucasian […]

PMCID: 4767573
PMID: 26808113
DOI: 10.1038/ng.3496

[…] identify which cell types significantly express sle candidate genes. specificity p-values were estimated based on the permutation of ranked expression levels for each locus (1010 permutations) using snpsea (, ). p-values (blue bars) that passed the multiple testing threshold (black line) show significant enrichment in sle loci. threshold lines are dependent on the number of categories present […]

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SNPsea institution(s)
Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA; Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
SNPsea funding source(s)
Supported by the National Institutes of Health (5K08AR055688, 1R01AR062886-01, 1U01HG0070033, T32 HG002295/HG/ NHGRI, 7T32HG002295-10), the Arthritis Foundation and the Doris Duke Foundation.

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