How to connect chr : position to rsid with UCSC genome browser / data?

[Peiyuan Zhu]

How to connect chr : position to rsid with UCSC genome browser / data?

[Gerardo Perez]

Hello,

Thank you for your interest in the Genome Browser and for sending your inquiry.

One option would be to extract the rsIDs using the Table Browser. On the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), make the following selections:

1. Set the group to "Variation"
2. Set the track to "dbSNP 155"
3. For common dbSNP's, set the table to “Common dbSnp(155) (dbSnp155Common)”. For all dbSNP's, set the table to “All dbSNP(155) (dbSnp155)”
4. Set the region to position and insert a position such as "chr8:102,551,589-102,561,018". You can also paste a list of regions by clicking “define regions”
5. Set the output format to “Selected fields from primary and related tables”. This will allow you to select fields of interest. The 'name' field contains the rsID for the variant.
6. Click "get output"
7. The output will then give you all the rsIDs for the region or regions.

If you have a bed file for the regions then you can use the bigBedToBed utility with the -bed option. You can download the bigBedToBed utility from the downloads page, https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads. You can then find bigBedToBed under the directory that matches your operating system. For example, here is the direct link for Linux: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed

You can run the utility on its own to see a help message, e.x.

$ ./bigBedToBed
bigBedToBed v1 - Convert from bigBed to ascii bed format.
usage:
   bigBedToBed input.bb output.bed
options:
   -chrom=chr1 - if set restrict output to given chromosome
   -start=N - if set, restrict output to only that over start
   -end=N - if set, restrict output to only that under end
   -bed=in.bed - restrict output to all regions in a BED file
   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs
   -header - output a autoSql-style header (starts with '#').
   -tsv - output a TSV header (without '#').

You can then run the bigBedToBed utility such as the following:

$ ./bigBedToBed -bed=in.bed https://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp155Common.bb output.bed

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

On Thu, Feb 22, 2024 at 2:31 PM Peiyuan Zhu <gary...@gmail.com> wrote:

How to connect chr : position to rsid with UCSC genome browser / data?

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