The query you are describing can also be performed using the
BioMart Martview interface (http://www.biomart.org/biomart/martview). As with the
R interface, this will include selecting datasets, filters and attributes.
Filters: To select SNPs from the 1000 Genome
Projects, you can set Variation Set Name
under General Variation Filters, and/or select Variation Set Name in the in the attributes. For SNP location,
select Chromosome, the Start and End in Region section (see answer 2 below for
To view the location of the SNPs, select Chromosome name and
Position on Chromosome (bp) in section: Variation>Sequence variation.
To answer your questions:
1.There are two Chromosome name attributes, one
under the Variation section, and one under the Sequences section. Because these
two sections are mutually exclusive (i.e. you can select one or the other), the
Chromosome name filter appears in both. These two Chromosome name attributes correspond
to numbers 2 and 54 on your list. Both attributes come from the same DB table,
so they should be identical.
2.The Start filter identifies SNPs starting at or
upstream of the entered bp. The End filters identifies SNPs located at or
downstream of the entered bp. Thus, for specific bp locations, you will need to
set both filters to be the same.
3.The majority of variants in Ensembl variation
are imported from NCBI dbSNP. Data from 1000 Genomes are included once it has
been submitted to dbSNP. You can see the source of the data by selecting
Variation Set Name in the attributes.
Please let me know if you have additional questions regarding this query or BioMart in general, and I will be glad to assist you in these matters.