How can I find a SNP related promoter, enhancer, TFBS and Gene ?

Question

[zihuguo1986]

Hi everyone! I am new to analysis the SNP data. Now I have get some SNP ids such as rs937395. The first step, I want to find the promoter, enhancer, TFBS and Gene influenced by this SNP. I mean I have obtained the location of this SNP on the chromosome, how can I find the promoter, enhancer, TFBS and Gene encompassed this location? The Second step, following the first, how can I find the promoter, enhancer, TFBS regulated Genes. I want to construct a regulated network from the SNP to the Gene I am interested. Thank you very much guys! Please excuse my poor English.

[Ashutosh Pandey]

Its not that easy task. But if you are looking for something to start with I would advise you to go to UCSC genome browser and search it with the rsID above. It has lots of regulatory tracks that give you peaks for different TFBS and other important regions. You can check if your SNP disrupts any of them. Its not that straighforward BTW. It will also show you the nearby genes.

[zihuguo1986]

Thank you very much, I will try this.

Answer 1

[Alex Reynolds]

You can use BEDOPS tools to query BED files that contain promoter, enhancer, TFBS and gene annotations, against a BED-formatted file that shows the position(s) of your SNP(s).

First, you could get a full list of SNPs into BED format.

Let's say you are using genome build hg19:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'SELECT chrom, chromStart, chromEnd, name FROM snp141Common' | tail -n +2 | sort-bed - > snp141Common.bed

You might filter this for your SNP of interest (e.g., rs937395):

$ grep -F 'rs937395' snp141Common.bed > rs937395.bed

If you have a text file of SNP IDs of interest, you could filter on matches with entries in that file:

$ grep -Ff snps_of_interest.txt snp141Common.bed > snps_of_interest.bed

Next, you might grab annotations of interest.

As an example, let's grab GENCODE v19 records, filter them for genes, and convert the result to BED with the gtf2bed conversion tool:

$ wget -O - ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz \
    | gunzip -c \
    | grep -w "gene" \
    | gtf2bed \
    > gencode.v19.genes.bed

To demonstrate a query, we can use the bedmap map tool to look at a 1 kb window around your particular SNP(s) of interest, looking for any GENCODE v19 gene ID annotations that fall within that window.

For instance, around rs937395:

$ bedmap --range 500 --echo --echo-map-id-uniq rs937395.bed gencode.v19.genes.bed > answer.bed

Or around all SNPs of interest:

$ bedmap --range 500 --echo --echo-map-id-uniq snps_of_interest.bed gencode.v19.genes.bed > answer.bed

Basically, you repeat and adjust this procedure depending on the window of interest, SNPs of interest, and target annotations of interest.