If you are already working in R:

1. Convert your snps to a GRanges object
2. Grab the locations of genes from a txdb object, from biomart, or from a UCSC track and convert to GRanges
3. Expand the boundaries of your genes by adding 10kb (see resize() in R)
4. Find overlapping SNPs using %over% between your two GRange objects.

You can use the Ensembl Variant Effect Predictor to see which genes are affected by your SNPs.

http://www.ensembl.org/info/docs/variation/vep/index.html

This is available as an online tool and as a Perl script. It will predict the consequences of each variant in the genes affected, giving you SO terms (see the link below). Variants within 5kb of a gene will be listed as upstream or downstream gene variants. You can also choose to get SIFT and PolyPhen scores for amino acid changes. And you can check if your variants have already been annotated in our database.

http://www.ensembl.org/info/docs/variation/predicted_data.html#consequences

If you really want to use a 10kb flank, there is a plugin that you can use with the VEP script that will allow you to change the flanks. You'll find it here:

https://github.com/ensembl-variation/VEP_plugins/blob/master/UpDownDistance.pm

Run as

perl variant_effect_predictor.pl -i input.txt -plugin UpDownDistance,10000

to set the distance to 10kb. Up/down distances can also be set separately:

perl variant_effect_predictor.pl -i input.txt -plugin UpDownDistance,10000,20000

sets up to 10kb and down to 20kb.

Both ncbi and ensembl have tools to do this.

I have been using ncbi 'eutils link' tools to get gene related snps in batch mode.

see if it can be helpful for you with little changes in the script.

#copied from NCBI efetch demonstration webpage

use LWP::Simple;
use LWP::UserAgent;
$db1 = 'gene';
$db2 = 'snp';
$linkname = 'gene_snp';

$base = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/';

#get the gene list from file

my $fname=shift;

open(pFILE,"<$fname")||die("error open genelist file\n");
while(<pFILE>){
    chomp;
    push @ids, $_;
}
#print @ids,"\n";
#assemble  the elink URL as an HTTP POST call

$url = $base . "elink.fcgi";

$url_params = "dbfrom=$db1&db=$db2&linkname=$linkname";
foreach $id (@ids) {
   $url_params .= "&id=$id";
}

#create HTTP user agent

$ua = new LWP::UserAgent;
$ua->agent("elink/1.0 " . $ua->agent);

#create HTTP request object

$req = new HTTP::Request POST => "$url";
$req->content_type('application/x-www-form-urlencoded');
$req->content("$url_params");

#post the HTTP request

$response = $ua->request($req); 
$output = $response->content;

open (OUT, ">snp_list.txt") || die "Can't open file!\n";

while ($output =~ /<LinkSet>(.*?)<\/LinkSet>/sg) {

$linkset = $1;
if ($linkset =~ /<IdList>(.*?)<\/IdList>/sg) {
      $input = $1;
      $input_id = $1 if ($input =~ /<Id>(\d+)<\/Id>/sg); 
}

while ($linkset =~ /<Link>(.*?)</Link>/sg) {
      $link = $1;
      push (@output, $1) if ($link =~ /<Id>(\d+)<\/Id>/);
   }

print OUT "$input_id:","\n";
    foreach(@output)
    {print OUT $_,"\n";}

}

close OUT;

If you just care about the coordinates of the genes +/- some window you can get a gene list from UCSC or Ensembl in .bed format and use BEDTools.

If you want all the bells and whistles, but not as much control over the windowing around your genes, you can use SNPEff

Are your SNPs in vcf format ? If so, you could tabix them and write something like:

for region in `write command to get genomic regions with genes in the format chr:start-end`;
do
tabix vcffile $region >> smaller.vcf;
done

I tried to use the Ensembl method above, but the input method appears to be based on chromosome position - forgive me if I am wrong about this as I am fairly new to all of this.

In essence, I have a list of SNPs by 'rs' number. Is there a simple tool that I can just dump the list of 'rs' numbers into that will return genes that they fall in or near? As I suggested 10kb either side would be nice but I'd be happy with 5kb if that is the default.

What I am looking for is pretty basic - put in 'rs' numbers and receive a list of gene symbols.

Thank you for your help and patience - as I have mentioned I am new to this. I have only recently made the jump from anthropology to genetics, so I would appreciate simplicity over all else!