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I am looking for a way to obtain SNP names from their coordinates (Chromosome:BP) - very much the reverse of the question answered here:

(https://stackoverflow.com/questions/20251612/map-snp-ids-to-genome-coordinates)

Example: I have identified that a SNP at position 64377836 on Chromosome 17 is associated with a certain factor in my analysis and would like to find out whether it has a SNP ID and what this ID is.

Manually, I can search databases for Chr17:64377836 and find rs668 - but I would like to find a way to do this automatically, preferably in R.

Is this possible in R - and if so, how?

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  • $\begingroup$ in what format you already have your input data? Is it a table, VCF? plink? $\endgroup$
    – JRodrigoF
    Commented Dec 8, 2022 at 12:09
  • $\begingroup$ In a table - but I could easily reformat it. $\endgroup$
    – Gux
    Commented Dec 8, 2022 at 12:16

1 Answer 1

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You can do this in R using the library biomaRt from Bioconductor. Here an example starting from a table with 3 columns: Chr, Start, End. Positions are assumed to be in GRCh38.

library(biomaRt)
snpMart = useEnsembl(biomart = "snps", 
             dataset = "hsapiens_snp")

# assuming your table is tab-separated, with column names
myData <- read.table("myTable.txt", sep="\t", header=True)

coords <- apply(myData, 1, paste, collapse = ":")


# submit the query
getBM(attributes = c('refsnp_id', 'chr_name', 'chrom_start', 'chrom_end', 'allele'),
  filters = c('chromosomal_region'), 
  values = coords, 
  mart = snpMart)

Source

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