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:
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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