Today I had a lunchtime discussion with some colleagues about the existence of poly-allelic Single Nucleotide Polymorphisms (SNPs). Quoting Wikipedia to explain what I mean:

>For example, two sequenced DNA fragments from different individuals, AAGC<strong>C</strong>TA to AAGC<strong>T</strong>TA, contain a difference in a single nucleotide. In this case we say that there are two alleles : C and T. Almost all common SNPs have only two alleles.

My point was that there could be some but I don't know any SNPs that have eg. 3 alleles such that there is either e.g. A/G/T, or all 4 bases in a population. If I wish to query a database, say BioMart, UCSC, HapMap for this, how would I do this?

If wanted to detect poly-allelic SNPs from sequencing data (*de novo*) using a reference sequence, which method/program could be used?

Edit: So far this seems to be real great stuff, got at least two different methods of getting the query right! 
But what about *de novo* (sorry, of course a reference sequence can be used, that's not really de novo) detection? Would for example [Maq](http://maq.sourceforge.net/) detect tri-allelic SNPs in short-reads?

You can query UCSC snp130 table. The fields of interest would be observed and class.
You can use their [public mysql server](http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29) and run this sql query:

    SELECT name,chrom,chromStart,chromEnd,observed,class,avHet
      FROM snp130
      WHERE length(observed)>3 and class="single" and avHet>0

I've added a condition to find only SNPs with average heterozygosity over zero. It finds 4949 SNPs in hg19, 490 are 4-allelic.