IL 10 SNP DATA
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Brijesh Dabhi
Dec 4, 2014, 11:11:55 AM12/4/14
to gen...@soe.ucsc.edu
cAN YOU SEND ME THE IL 10 GENE SNP DATA?
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BRIJESH DABHI
Ph.D SCHOLAR
ASHOK & RITA PATEL INSTITUTE OF INTEGRATED STUDIES AND RESEARCH IN BIOTECHNOLOGY & ALLIED SCIENCES
NEW V V NAGAR
PH. 98 242 77 683
Matthew Speir
Dec 4, 2014, 7:15:34 PM12/4/14
to Brijesh Dabhi, gen...@soe.ucsc.edu
Hi Brijesh,
Thank you for your question about getting SNP data for the IL10 gene. There are many different variation tracks available for the hg19 assembly of the human genome, http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19. These variation tracks are separated into two track groups in the UCSC Genome Browser, the "Phenotype and Literature" group and the "Variation" group. SNP tracks under "Phenotype and Literature", such as OMIM AV SNPs or ClinVar Variants, contain variants that have been associated with a disease phenotype. Most of the SNP tracks under "Variation", such as All SNPs(141) or EVS Variants, contain SNPs and other variants from various SNP data repositories. If you are interested in any and all SNPs that may occur in the IL10 gene, then you will mostly likely be interested in the All SNPs(141) track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=snp141, which contains SNPs from the dbSNP 141 release.
You can get the SNPs from the All SNPs(141) track that occur in both the exons and introns of the IL10 gene using the Table Browser. To get this information, use the following steps:
1. Navigate to the Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables.
2. Select your assembly and tracks
clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Variation
track: All SNPs(141)
table: snp141
region: click the button next to position, and the enter the position: chr1:206,940,948-206,945,839
output: all fields from selected table
output file: enter a file name to save your results to a file, or leave blank to display results in your browser
3. Click "get output".
You can see an explanation of what the various columns in your output represent by clicking the "describe table schema" button on the Table Browser after you've selected the snp141 table. You can also replace the track and table with your variation track of interest if the All SNPs(141) track does not fit your need.
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.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about getting SNP data for the IL10 gene. There are many different variation tracks available for the hg19 assembly of the human genome, http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19. These variation tracks are separated into two track groups in the UCSC Genome Browser, the "Phenotype and Literature" group and the "Variation" group. SNP tracks under "Phenotype and Literature", such as OMIM AV SNPs or ClinVar Variants, contain variants that have been associated with a disease phenotype. Most of the SNP tracks under "Variation", such as All SNPs(141) or EVS Variants, contain SNPs and other variants from various SNP data repositories. If you are interested in any and all SNPs that may occur in the IL10 gene, then you will mostly likely be interested in the All SNPs(141) track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=snp141, which contains SNPs from the dbSNP 141 release.
You can get the SNPs from the All SNPs(141) track that occur in both the exons and introns of the IL10 gene using the Table Browser. To get this information, use the following steps:
1. Navigate to the Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables.
2. Select your assembly and tracks
clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Variation
track: All SNPs(141)
table: snp141
region: click the button next to position, and the enter the position: chr1:206,940,948-206,945,839
output: all fields from selected table
output file: enter a file name to save your results to a file, or leave blank to display results in your browser
3. Click "get output".
You can see an explanation of what the various columns in your output represent by clicking the "describe table schema" button on the Table Browser after you've selected the snp141 table. You can also replace the track and table with your variation track of interest if the All SNPs(141) track does not fit your need.
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.
Matthew Speir
UCSC Genome Bioinformatics Group
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