Dbsnp - Querying Chun And Chnoton

Question

[Andrea_Bio]

Hello

dbSNP makes the distinction between snps which are classed as chUn (variations on unplaced chromosomes) and chNotOn (variations which aren't mapped to any chromosomes)

I am trying to query these 2 types of snp using the dnSNP limits but the only related term i can find is Un[CHR]. I don't know if this clause returns just chUn or both chUn and chNotOn. It's name suggests the former.

There is no such term as NotOn[CHR]

Ideally i would like to know:

Quesiton 1 a) are there separate clauses for chUn and chNotOn b) what are they :) c) what does Un[CHR] retrieve: chUn, chNotOn or both? I don't think it is both because of the queries you will see below

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snp rs412 is classed as Un chromosome on the website but i don't know if this means chUn or ChNotOn or either

but this query does not return any results: rs412[All Fields] AND Un[CHR]

Neither is it in the results of this query: "un"[CHR] AND "homo sapiens"[Organism] AND "snp"[Snp_Class]

Question 2 What does Un mean on the website when it describes a snp mapping

Question 3 Also do you know how ensembl variation database handles these 2 types of snp. I am not sure but i think it treats both categories in the same fashion as unmapped SNPs. In other words, for those familiar with the schema, they are not related to variation features.

many thanks

ps: my guess is that the limit un[chr] retrieves unplaced chromsomes only (unchr) whereas the Un term on the website describes all unmapped chromosomes = [unchr + chrNotOn] and that rs412 is a chNotOn

Answer 1

[Larry_Parnell]

Andrea,

One way to determine if SNP rs412 maps to an unmapped genomic segment or does not map to the genome is to perform a BLASTN search with the SNP sequence. I would use a query of 121 bp with the polymorphic site set at position 61. Look to see which type of genomic fragment you see in the BLAST results.

My belief is "Un" on the website means that the segment or sequence in question maps to a fragment of the genome that has yet to be assigned to a chromosome. Keep in mind that the human genome is not 100% complete and gaps in the reference sequence could contain a SNP that has been identified by other projects. Also, the source of the DNA for the SNP identification could have an insertion sequence that has not been mapped to the reference genome with absolute certainty.