Finding Snps In A Given Range Using Dbsnp/Entrez

Question

[Pierre Lindenbaum]

Hi All,

is there a way to find the SNPs by their positions for a given genomic assembly using ENTREZ ? For example, on hg18/ncbi36 rs25 is located at chr7:11550417-11550917 . How can I find it using entrez ? I tried something like:

7[CHR] AND 11550407:11550427[CHRPOS] AND txid9606[TAX_ID]

but I got no result, guess it's because entrez uses hg19/ncbi37 by default (?)

Any idea ?

Thanks,

Pierre

Answer 1

[Neilfws]

I don't think it's possible to select chromosomal position based on an older genome build. Here is a list of all fields that you can use in a dbSNP query:

ALL,All Fields,All terms from all searchable fields
UID,UID,Unique number assigned to publication
FILT,Filter,Limits the records
RS,Reference SNP ID,Clustered SNP ID (rs)
CHR,Chromosome,chromosomes
GENE,Gene Name,locus link symbol
HAN,Submitter Handle,Submitter Handle
ACCN,Accession,nucleotide accessions
LLID,LocusLink ID,locus link UID
ORGN,Organism,Organism
FXN,Function Class,Function class
GTYP,Genotype,Genotype info
NREF,Not reference assembly,SNP not mapped to reference assembly
HETZ,Heterozygosity,Heterozygosity
MPWT,Map Weight,Map weight
VALI,Validation Status,Validation status
SRAT,Success Rate,Success rate
CBID,Create Build ID,Original Build ID
UBID,Update Build ID,Update Build ID
PDAT,Publication Date,SNP Publication date
MDAT,Modification Date,SNP modification date
PCLS,Population Class,Population classification based on geographic location
MCLS,Method Class,Assay Method
SS,Submitter SNP ID,Submitter ID
SID,Local SNP ID,Local SNP ID
VARI,Allele,Allele
SCLS,SNP Class,SNP class
GDSC,Gene Description,description of gene
CPOS,Base Position,Chromosome base position
GPOS,Contig Position,Contig base position
WORD,Text Word,Free text associated with record
WTAA,Reference Amino Acid,Reference Amino Acid
MTAA,Variant Amino Acid,Variant or Mutant Amino Acid
RSNP,Reference SNP,Reference SNP
SIDX,SNP Index,SNP Index

I get results returned for queries such as:

7[CHR] AND Homo sapiens[ORGN] AND 132[UBID] AND 11500000:11700000[CPOS] AND 36[CBID]

but they do not include rs25. I assume that "Created/Updated in build" on the dbSNP page for an individual SNP refers to dbSNP build, rather than genome build.

Answer 2

[Mary]

This was actually a big concern of mine in a recent meeting talking about some cloud applications. The assembly and software version choices were not available to the end user. This was supposedly a "feature" that you are getting the most updated software and current assembly. But it isn't always what you need [/end rant].

That said, I know you want to use Entrez, but UCSC offers access to old assemblies. The ones that aren't readily available from the menu may be accessible from their archives page I can see rs25 in the Human Nov. 2002 Assembly at chr7:11,223,514-11,233,514.

[Pierre Lindenbaum]

Thanks Mary, but I my case, I wanted to use the SOAP/WSDL web service from the NCBI to show my students how to generate a java SOAP client and annotate a set of genomic positions.

Answer 3

[Prabhakaran]

Well i have a problem in finding the rsID for a particular SNP whose nucleotide position is cited in literature(not rsID).For example ADRA1D T1848A.so If i want to work on this SNP i indeed need the rsID for this.So please help me out in solving this problem..

[Pierre Lindenbaum]

ask a new question please.