Getting Genes For Snps From Ucsc Browser

Question

[jvijai]

I tried to get gene-names for a list of SNPs using the UCSC table browser using sql However, I do not get the gene names either 3' or 5' of the SNP position.

1. I would like to get the nearest gene(s)(upstream or downstream 500kb) for a given SNP.
2. I would like to query the table GWAS Catalog and filter only for those associated with "cancer".

Can someone help me.
Thanks

Answer 1

[Pierre Lindenbaum]

• to find the SNP at 500k of a given gene, see this previous question: How To Map A Snp To A Gene Around +/- 60Kb ?
• for the second question, the SQL query could be

~> mysql  -h  genome-mysql.cse.ucsc.edu -A -u genome -D hg19 \
  -e 'select * from gwasCatalog as G where  (G.title like "%cancer%" or G.trait like "%cancer%" ) \G'


    *************************** 1. row ***************************
           bin: 756
         chrom: chr1
    chromStart: 22490723
      chromEnd: 22490724
          name: rs7521902
      pubMedID: 20852632
        author: Goode
       pubDate: 2010-09-19
       journal: Nat Genet
         title: A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24
         trait: Ovarian cancer
    initSample: 1,768 European ancestry cases, 2,354 European ancestry controls
    replSample: 8,709 European ancestry cases, 51,764 European ancestry controls
        region: 1p36.12
         genes: NR
    riskAllele: rs7521902-?
    riskAlFreq: NR
        pValue: 5E-6
    pValueDesc:
      orOrBeta:    1.12
          ci95: [1.07-1.18]
      platform: Illumina [2,056,878] (imputed)
           cnv: N
    *************************** 2. row ***************************
           bin: 1510
         chrom: chr1
    chromStart: 121280612
      chromEnd: 121280613
          name: rs11249433
      pubMedID: 19330030
        author: Thomas
       pubDate: 2009-03-29
       journal: Nat Genet
         title: A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1).
         trait: Breast cancer
    initSample: 1,145 cases, 1,142 controls
    replSample: 8,625 cases, 9,657 controls
        region: 1p11.2
         genes: Intergenic
    riskAllele: rs11249433-C
    riskAlFreq: 0.39
        pValue: 7E-10
    pValueDesc:
      orOrBeta:    1.16
          ci95: [1.09-1.24]
      platform: Illumina [528,173]
           cnv: N
    (...)

[Pierre Lindenbaum]

You can't: "The file is created on the server host, so you must have the FILE privilege to use this syntax."

[jvijai]

Pierre, That works great! However, being a SQL newbie, can you write the part required to redirect the output to a text file. I tried using 'INTO OUTFILE' but did not work for me.

[Pierre Lindenbaum]

Using unix:

yourcommand > file.txt

[Pierre Lindenbaum]

http://www.december.com/unix/tutor/redirect.html

[jvijai]

How to add 'into dumpfile' to this command

[jvijai]

Thanks Pierre. Much appreciated.