Identify SNP from genetic position

Question

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?

Answer 1

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