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.

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

Data contributions are actively sought: Raw data controbutions are welcome from all sources on data sheets containing original SNP names and dbSNP@(EVA/NCBI) returned `rs` numbers. Your kind contributions will be credited as shown below. Please contact us to proceed.

The repository data summary

SNP rs to name matches

Species	SNP Counts	Data sources
Cattle	5,785,881	1, 2, 3, 4, 8
Chicken	576,203	1, 6
Horse	109,323	1
Pig	711,093	1, 5
Rainbow trout	63,177	7, 10
Sheep	610,853	1
〈 SUM 〉	7,856,530

SNP rs to ss number matches

Species	SNP Counts	Data sources
Cattle	4,312,828	1, 2, 3
Horse	67,855	1
Pig	64,232	5
Sheep	610,853	1
〈 SUM 〉	5,055,768

Batch data

Data for batch query will be available upon request.

Data sources and acknowledgements

1.	Data: 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.	Data: 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.	Data: 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] Known issue: 11 of 999 SNP names do not have a valid rs number
4.	Data: 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) Known issue: 51,881 of 1,673,553 SNP names do not have a valid rs number
5.	Data: 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.	Data: File "hansCheng.snp.txt" received in 2007 Source: Hans Cheng (hans.cheng@usda.gov) (2007)
7.	Data: Data file received on April 28, 2020 Source: "Mohamed Salem" [Mohamed.Salem@mtsu.edu] (2020)
8.	Data: 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.	Data: Cattle 58K SNP mapping info received in 2009 Source: "James Reecy" [jreecy@iastate.edu] (2009)
10.	Data: 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)

Contacts

Zhi-Liang Hu (zhu@iastate.edu)

Data updates

Created: June 08, 2020
Last data contribution received: July 16, 2021
Last change to keep this service updated: May 23, 2024

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Search SNP:	Names
Search SNP:	SS numbers

Contacts Zhi-Liang Hu (zhu@iastate.edu)	Data updates Created: June 08, 2020 Last data contribution received: July 16, 2021 Last change to keep this service updated: May 23, 2024
Request citing the use of this service: Please follow the examples given in this FAQ to cite the use of this service.