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The purpose of this effort is to collect all variant SNP names that occur during the processes including but not limited to SNP discovery, utility development, and data integrations, usually before they were submitted to dbSNP but have been widely used. The direct push for such efforts are mainly from the needs of data annotations and/or data integrations when SNP name match information are hard to find in publicly available resources.


SNP rs to name matches

Data countsSpeciesData sources
5,785,881cattle1, 2, 3, 4, 8
576,203chicken1, 6
109,323horse1
711,093pig1, 5
32,928rainbow trout7
610,853sheep1
7,826,281<= sum

SNP rs to ss number matches

Data countsSpeciesData sources
4,312,828cattle1, 2, 3
67,855horse1
64,232pig5
610,853sheep1
5,055,768<= sum

Utilities

  • Data annotations
    • Animal QTLdb
      Data curation
  • Data Integrations

Data sources

1.SNPchiMp v.3, integrating and standardizing single nucleotide polymorphism data for livestock species (DATABASE: http://bioinformatics.tecnoparco.org/SNPchimp/; Publication: PMID: 25881165, DOI: https://doi.org/10.1186/s12864-015-1497-1; Journal: BMC Genomics 2015)

Source: http://bioinformatics.tecnoparco.org/SNPchimp/index.php/download (accessed 2020-06-07)

DATA:/data/pub/tools/SNPchimp/SNPchimp_{cattle,chicken,horse,pig,sheep};
PROC:~/db/SNPinfo/
Setup: 2020-06-08 10:32:48
Contributions to the data set:

  • 'RS' to name matches: //cattle: 1,393,893; //chicken: 573,210; //horse: 109,323; //pig: 705,986; //sheep: 610,853;
  • 'RS' to 'SS' matches: //cattle: 782,979; //horse: 67,855; //sheep: 610,853;
2.770K HD SNP chip: Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor (BMC Bioinformatics 26(16):2069-70(2010): https://academic.oup.com/bioinformatics/article/26/16/2069/217748 PMID:20562413; DOI: https://doi.org/10.1093/bioinformatics/btq330

Source: Illumina BeadChip, https://www.illumina.com/documents/products/datasheets/datasheet_bovineHD.pdf; Forwarded by James Koltes [jekoltes@mail.iastate.edu] March 25, 2012

DATA:~/db/QTLdb/cattle_data/snpHD/BovineHD_rs-ss-name-map.xls;
PROC:~/db/SNPinfo/
Setup: 2020-08-31 16:55:11
Contributions to the data set:

  • 'RS' to name matches: //cattle: 2,700,250;
  • 'RS' to 'SS' matches: //cattle: 3,521,736;
3.770K HD SNP chip: Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor (BMC Bioinformatics 26(16):2069-70(2010): https://academic.oup.com/bioinformatics/article/26/16/2069/217748 PMID:20562413; DOI: https://doi.org/10.1093/bioinformatics/btq330

Source: Cattle High Density SNP Chip Consortium; file sent by Robert Schnabel [schnabelr@missouri.edu]

DATA:~/db/QTLdb/cattle_data/snpHD/BovineHD_rs_111105.csv;
PROC:~/db/SNPinfo/
Setup: 2020-08-31 17:24:25
Contributions to the data set:

  • 'RS' to name matches: //cattle: 999;
  • 'RS' to 'SS' matches: //cattle: 8,113;
4.SNPs from the Baylor Center of Medicine - Human Genome Sequencing Center (BCM-HGSC) cattle genome sequencing project (2007)

Source: ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/snp/Btau20070913/ (accessed in 2007)

DATA:~/db/QTLdb/cattle_data/snp/balorSNP_bov/Btau20070913.dat;
PROC:~/db/SNPinfo/
Setup: 2020-08-31 18:10:21
Contributions to the data set:

  • 'RS' to name matches: //cattle: 1,673,553;
  • 'RS' to 'SS' matches:
5.Pig 60k SNP chip: Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology (PLoS One. 2009; 4(8): e6524, https://dx.doi.org/10.1371%2Fjournal.pone.0006524)

Source: Martien Groenen [martien.groenen@wur.nl] (2012)

DATA:~/db/QTLdb/pig_develop/pig_snp/snpChip_pig/Pig60K_ss_rsNumbers.txt;
PROC:~/db/SNPinfo/
Setup: 2020-08-31 18:27:46
Contributions to the data set:

  • 'RS' to name matches: //pig: 5,107;
  • 'RS' to 'SS' matches: //pig: 64,232;
6.File "hansCheng.snp.txt" received in 2007

Source: Hans Cheng (hans.cheng@usda.gov) (2007)

DATA:~/db/QTLdb/chicken_data/snp/hansCheng.snp.txt;
PROC:~/db/SNPinfo/
Setup: 2020-08-31 18:45:25
Contributions to the data set:

  • 'RS' to name matches: //chicken: 2,993;
  • 'RS' to 'SS' matches:
7.Data file received on April 28, 2020

Source: "Mohamed Salem" [Mohamed.Salem@mtsu.edu] (2020)

DATA:~/db/QTLdb/rainbow_trout/SNPs_nm-rs/Mohamed_Salem/combined-probID-rs.txt;
PROC:~/db/SNPinfo/
Setup: 2020-08-31 19:41:13
Contributions to the data set:

  • 'RS' to name matches: //rainbow trout: 32,928;
  • 'RS' to 'SS' matches:
8.Redundent SNP names handled within Council on Dairy Cattle Breeding (CDCB)

Source: Received from George Wiggans (george.wiggans@uscdcb.com) on Oct. 3, 2020

DATA:/data/pub/tools/SNPusCDCB/;
PROC:/data/pub/tools/SNPusCDCB/
Setup: 2020-10-06 14:51:49
Contributions to the data set:

  • 'RS' to name matches: //cattle: 17,186;
  • 'RS' to 'SS' matches:
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Contact: NAGRP Bioinformatics Team
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