Livestock SNP IDs/names match repository

This collection of 7,856,530 known SNP IDs/names and 5,055,768 SNP 'rs' to 'ss' ID matches are from the SNP discovery, utility development, data integrations, and other processes along the path in which the final confirmed SNP information were eventually submitted to dbSNP. SNP information in this repository were contributed by individuals and groups are listed below in the "Data sources and acknowledgement" section.

Since the SNP IDs/custom names have been widely used in published data sets (usually prior to their submission to dbSNP), the SNP identity matches are essential for data alignments or connectivity in terms of annotations, integrations, and mining of genome to phenome analysis involving SNPs.

We welcome new data contributions to this SNP name/ID match repository. The information we look for include SNP temporary or internal development IDs, custom names, and other identifiers that match to SNP 'rs' IDs, as well as flanking sequences (which will allow us to match them using an in-house procedure). Your contribuitions will be acknowledged as one of the data sources as listed below.

Search SNP: Names
SS numbers
Example SNP names: BTR-chr1_140052934
CHR1-140052934
LGT-BLACK-ANG01-161672
BovineHD1500009775
oar3_OAR4_49000270
BTR-chr1_140053896
CHR1-140053896
BovineHD0700006387
BTA1-139351597
1_139351597
BTB-01305638
OAR12_18620966.1
CHR1-140067636
1_139367048
BTA1-139390026
AX-169688440
AX-169712526
CHR1-140094055
BTA1-139393445
RMC_1_140094055

The repository data summary

SNP rs to name matches
SpeciesSNP CountsData sources
Cattle5,785,8811, 2, 3, 4, 8
Chicken576,2031, 6
Horse109,3231
Pig711,0931, 5
Rainbow trout63,1777, 10
Sheep610,8531
〈 SUM 〉7,856,530
SNP rs to ss number matches
SpeciesSNP CountsData sources
Cattle4,312,8281, 2, 3
Horse67,8551
Pig64,2325
Sheep610,8531
〈 SUM 〉5,055,768

 

Batch data

Data for batch download will be available upon request.

 

Data sources and acknowledgements

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)

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

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]

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)

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)

6. File "hansCheng.snp.txt" received in 2007

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

7. Data file received on April 28, 2020

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

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

9. Cattle 58K SNP mapping info received in 2009

Source: "James Reecy" [jreecy@iastate.edu] (2009)

10. Rainbow trout Axiom_Omy50Kv2 SNP blast match to Dec. 2020 SNP downloads from EVA/dbSNP (unmapped data, rs assigned)

Source: SNP chip data with flanking seqs are from "Gao, Guangtu" [guangtu.gao@usda.gov] and "Palti, Yniv" [yniv.palti@usda.gov]; NAGRP Pipline for SNP matches using flanking sequences by Zhiliang Hu [zhu@iastate.edu] (2021)

Contact

Zhiliang Hu (zhu@iastate.edu)

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Contact: NAGRP Bioinformatics Team
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