Can there be more than one SNP genomic location?

[ramiromagno]

I see that the type of the locations element of the JSON response for singleNucleotidePolymorphisms is Array. The description of this element reads

The SNP’s genomic locations.

I thought a SNP could have only one genomic location but this design pattern hints otherwise. Could you please clarify?

[cmalangone]

Please find more details about the status of this issue here:
https://www.ebi.ac.uk/panda/jira/browse/GOCI-2441

[ramiromagno]

@cmalangone: It seems the only situations that I have come across that include more than one genomic location are those where SNPs are being mapped also to either:

• GRC assembly patches
• haplotype (HAPs)
• pseudo autosomal regions (PARs)

For example, check out the following SNPs:

rs10910092

     chromosomeName chromosomePosition region.name                                                             _links.snps.href
1                 1            2570077     1p36.32 https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs10910092
2 CHR_HSCHR1_1_CTG3            2570077        <NA> https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs10910092

rs570398477

     chromosomeName chromosomePosition region.name                                                              _links.snps.href
1                 2            1348118      2p25.3 https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs570398477
2 CHR_HSCHR2_4_CTG1            1346312        <NA> https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs570398477

Should we not stick with the traditional autosomal + sex chromosomes, and perhaps the mitochondrial one only?? It seems you've adopted that criterion anyway for the web version of the GWAS Catalog:

• https://www.ebi.ac.uk/gwas/variants/rs10910092
• https://www.ebi.ac.uk/gwas/variants/rs570398477