rbioinformaticsbioconductorgeneticsgenome

Map SNP IDs to genome coordinates

I have several SNP IDs (i.e., rs16828074, rs17232800, etc...), I want to their coordinates in a Hg19 genome from UCSC genome website.

I would prefer using R to accomplish this goal. How to do that?

Solution

  • Here is a solution using the Bioconductor package biomaRt. It is a slightly corrected and reformatted version of the previously posted code.

    library(biomaRt) # biomaRt_2.30.0

snp_mart = useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp")

snp_ids = c("rs16828074", "rs17232800")
snp_attributes = c("refsnp_id", "chr_name", "chrom_start")

snp_locations = getBM(attributes=snp_attributes, filters="snp_filter", 
                      values=snp_ids, mart=snp_mart)

snp_locations
#    refsnp_id chr_name chrom_start
# 1 rs16828074        2   232318754
# 2 rs17232800       18    66292259

    Users are encouraged to read the comprehensive biomaRt vignette and experiment with the following biomaRt functions:

    listFilters(snp_mart)
listAttributes(snp_mart)
attributePages(snp_mart)
listDatasets(snp_mart)
listMarts()