Query about finding SNPs within a Regulatory Region using ENCODE

[Kausik Ganguly]

SIr, how can we use UCSC genome browser and ENCODE project related tools to find out Single Nucleotide Polymorphisms (SNPs) that are residing within a particular Genomic co-ordinate range, which is shown to be regulatory from the "Regulatory Elements Database" (Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res. 2013 May;23(5):777-88. PMID: 23482648; PMCID: PMC3638134)?

For example when we searched for BRCA1 gene in Regulatory Elements Database, we got Top 10 Correlated DHS sites, under which we searched the region >

Location	Cluster	P-value
chr17:41132840-41132990	333	0.001

Now, we wish to know if there is any SNP within the range chr17:41132840-41132990, using UCSC genome browser tool.

We will be highly obliged with your kind co-operation;

Kausik Ganguly,

Research Fellow,

Dept. of Genetics,

Dr. Mainak Sengupta's Lab,

University of Calcutta.

[Steve Heitner]

Hello, Kausik.

You can list SNPs at specific genomic loci using our Table Browser.  If you are unfamiliar with the Table Browser, please see the User’s Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.

To look up SNPs, perform the following steps:

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables

2. Enter the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Variation
Track: Common SNPs(138)
Table: snp138Common
Region: Enter your coordinates in the “position” box
Output format: all fields from selected table

3. Click the “get output” button

In this particular case, there do not appear to be any SNPs at chr17:41,132,840-41,132,990.  This can be confirmed by viewing the Common SNPs(138) track at these coordinates in the Browser.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  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.

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Steve Heitner
UCSC Genome Bioinformatics Group

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[Steve Heitner]

Hello again, Kausik.

Just as a follow-up, if you would like to query multiple loci, there is a “define regions” button on the “region” line that will allow you to specify multiple loci in a single query.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users.  If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group