There are a few options:
The tool " Phenotype Association -> SIFT" will accept an input file of
variant locations/alleles and retrieve annotations, including OMIM
Alternatively, you could label your variants by rs identifiers (or
perhaps you already have these), or just use genomic coordinates, to
intersect with the GWAS Catalog dataset.
The general path would be to obtain the most recent dbSNP and GWAS
Catalog tracks from the UCSC Table Browser ("Get Data -> UCSC Main",
genome to be hg19, then under the group "Varation and Repeats", dbSNP
135 and GWAS are both listed as tables under the dbSNP track - get
it will require two queries). You may be joining on common keys (such
rs numbers) or overlapping genomic coordinates, depending on the
starting data format and how you choose to do the intersect.
For tool help, the first protocol in the "Using Galaxy" paper &
supplemental walks through how to extract data from the UCSC Table
browser and join data by various methods. The protocol's goal is
different from your goal, but the methods will be similar to what you
will be doing. The second protocol has even more examples for
and formatting datasets, if you want to manipulate datasets to
I am assuming that you are using a human, hg19 dataset, but if you
another, SIFT will not be possible. Still, UCSC may have analogous
tracks to select from, depending on the genome. Or you could try
BioMart, or one of the other sources under "Get Data", if these have
your data. You can also always directly import (upload or FTP) a
reference dataset of known SNP Phenotypes from any source, mapped to
your target genome, and use Galaxy's tools to perform the intersection
and file manipulations.
Hopefully this helps to get you started!