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SNPchiMp specifications


Unique identifier OMICS_08305
Name SNPchiMp
Restrictions to use None
Database management system MySQL
Version 3.0
Maintained Yes


  • Mammals
    • Bos taurus


  • person_outline Ezequiel L. Nicolazzi

Publications for SNPchiMp

SNPchiMp citations


Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

PLoS One
PMCID: 5844516
PMID: 29522525
DOI: 10.1371/journal.pone.0190184

[…] ing GenABEL package [] in R environment, and polymorphisms with a minimum allele frequency (MAF) < 0.05 were discarded for further analysis. In order to be able to compare data from the two platforms SNPchiMp v.3 [] was used to select SNPs overlapping between both. […]


Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs

PLoS One
PMCID: 5811030
PMID: 29438444
DOI: 10.1371/journal.pone.0192673

[…] osomes, were obtained by the R package biomaRt (v. 2.30.0) [, ] from the Sus scrofa genome build (10.2, version 79). The chromosomal locations of the SNPs associated with the eQTLs were obtained from SNPchiMp (v. 3) database []. The chromosomal densities of eQTLs were calculated by the number of either unfiltered or filtered eQTLs per chromosome divided by length in bases of the respective chromos […]


Identification of Candidate Genes for Reactivity in Guzerat (Bos indicus) Cattle: A Genome Wide Association Study

PLoS One
PMCID: 5268462
PMID: 28125592
DOI: 10.1371/journal.pone.0169163
call_split See protocol

[…] Map positions of the SNPs were based on UMD3.1. Information about the markers (rs, map position, alleles) were obtained using the SNPchiMp tool []. When these SNPs were located within a gene, several analyses were carried out. First, the position of the SNP (intronic or exonic, 5´-UTR or 3´-UTR) was determined. Second, repercuss […]


SNP and haplotype based genome wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population

BMC Genet
PMCID: 4837538
PMID: 27094516
DOI: 10.1186/s12863-016-0368-3

[…] cance thresholds defined by the Bonferroni correction was too conservative. Therefore, the genome-wide suggestive threshold was also defined as; P = 5.0 × 10−5. SNP maps were updated according to the SNPchiMp v.2 database [] and the Sscrofa 10.2 assembly. The positional candidate genes within the range of 1 Mb bin size of the significant region were scanned using the NCBI2R R-package []. r2 values […]


The Use of Kosher Phenotyping for Mapping QTL Affecting Susceptibility to Bovine Respiratory Disease

PLoS One
PMCID: 4831767
PMID: 27077383
DOI: 10.1371/journal.pone.0153423
call_split See protocol

[…] The SNPchiMp database [] was used to convert the Illumina SNP name to the rsID (the SNP accession number used to search a SNP in all public databases). The rsID was used in NCBI database (http://www.ncbi. […]


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SNPchiMp institution(s)
Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc Cascina Codazza, Lodi, Italy

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