Variant Annotation Integrator help

[Curbelo Montañez, Casimiro]

Hi,

 

My name is Aday and I am a student at Liverpool John Moores University, UK.

 

I am trying to find out the nearest gene and distance for two SNPs (rs4361859 and rs763727). I am using the Variant Annotation Integrator tool with the following criteria:

 

• Clade: Mammal
• Genome: Human
• Assembly: Feb. 2009 (GRCh37/hg19)
• Region to annotate: Genome
• Select Genes: UCSC Genes (RefSeq, GenBank….)

 

This is the output I obtained:

 

## ENSEMBL VARIANT EFFECT PREDICTOR format (UCSC Variant Annotation Integrator)

## Output produced at 2017-11-03 08:44:45

## Connected to UCSC database hg19

## Variants: Variant Identifiers

## Transcripts: UCSC Genes (RefSeq, GenBank, CCDS, Rfam, tRNAs & Comparative Genomics) (hg19.knownGene)

## dbSNP: Simple Nucleotide Polymorphisms (dbSNP 150) (/gbdb/hg19/vai/snp150.bed4.bb)

## Keys for Extra column items:

## SIFT: (http://sift.bii.a-star.edu.sg/) SIFT (D = damaging, T = tolerated)

## PP2HVAR: (http://genetics.bwh.harvard.edu/pph2/) PolyPhen-2 with HumVar training set (D = probably damaging, P = possibly damaging, B = benign)

## PP2HDIV: (http://genetics.bwh.harvard.edu/pph2/) PolyPhen-2 with HumDiv training set (D = probably damaging, P = possibly damaging, B = benign)

Uploaded Variation     Location       Allele  Gene    Feature Feature type    Consequence    Position in cDNA       Position in CDS Position in protein     Amino acid change      Codon change   Co-located Variation      Extra

rs763727       chr16:83342301 A       CDH13   uc010vns.2        Transcript     intron_variant -       -       -       -       -        rs763727       INTRON=6/14

rs763727       chr16:83342301 A       CDH13   uc002fgx.3        Transcript     intron_variant -       -       -       -       -        rs763727       INTRON=5/13

rs763727       chr16:83342301 A       CDH13   uc010vnt.2        Transcript     intron_variant -       -       -       -       -        rs763727       INTRON=4/12

rs763727       chr16:83342301 A       CDH13   uc010vnu.2        Transcript     intron_variant -       -       -       -       -        rs763727       INTRON=4/12

rs4361859      chr9:99824697  A       CTSL2   uc004awu.3        Transcript     upstream_gene_variant  -       -       -       -        -       rs4361859      DISTANCE=2530

 

Would it be correct saying that the variant rs4361859 is located ~2.5 kb upstream of the gene CTSL2? I am not too sure whether the column “Extra” for this variant indicates the actual distance from the nearest gene or not.

 

Any help will be appreciated.

 

Kind Regards,

 

Aday

 

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[Matthew Speir]

Hi Aday,

Thank you for your question about the Variant Annotation Integrator (VAI) in the UCSC Genome Browser.

You are correct, the "DISTANCE" entry in the "Extra" column of your output indicates the distance from the SNP to the gene.

The VAI will look for and report variants that are within 5000 bases of each transcript. If your variants are farther than that, then they won't be reported. If you'd like to find the nearest gene for each variant, regardless of distance, you may be interested in the script on the following GenomeWiki page: http://genomewiki.cse.ucsc.edu/index.php/Finding_nearby_genes.

I hope this is helpful. If you have any further questions, please reply to genome...@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

Important Notice: the information in this email and any attachments is for the sole use of the intended recipient(s). If you are not an intended recipient, or a person responsible for delivering it to an intended recipient, you should delete it from your system immediately without disclosing its contents elsewhere and advise the sender by returning the email or by telephoning a number contained in the body of the email. No responsibility is accepted for loss or damage arising from viruses or changes made to this message after it was sent. The views contained in this email are those of the author and not necessarily those of Liverpool John Moores University. --

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