I don't find this question particularly clear.  I believe the key resources
will be the
IlluminaHumanMethylation450k.db packages and the appropriate
SNPlocs.Hsapiens.dbSNP.* SNP
location package.

Once you have installed IlluminaHumanMethylation450k.db, you can use SQL
queries to obtain information about the probes or associated islands.  The
vignette of the package is also relevant.  Coordinates are given for probes,
against two genome builds.  Some information relevant to your concern may be
in the "snp" and "snp10" columns but I do not know where these are
documented.

After installing and attaching IlluminaHumanMethylation450k.db, one way to
proceed is

> con = IlluminaHumanMethylation450k_dbconn()
> dbListTables(con)
 [1] "accessions"     "controlprobes"  "cpgi"           "cpgilocation"
 [5] "cpgirelations"  "cpgislandnames" "cpgiview"       "dmr"
 [9] "fantom"         "featuregroups"  "featurenames"   "map_counts"
[13] "map_metadata"   "metadata"       "probedesign"    "probedesign1"
[17] "probedesign2"   "probelocation"  "probes"         "probesummary"
[21] "reglocation"    "regulatory"     "regview"        "relations"
[25] "snps"           "sqlite_stat1"
> dbGetQuery(con, "select * from probedesign limit 5")
  row_names   Probe_ID Infinium_Design_Type AddressA_ID AddressB_ID
1         1 cg00035864                   II    31729416
2         2 cg00050873                    I    32735311    31717405
3         3 cg00061679                   II    28780415
4         4 cg00063477                   II    16712347
5         5 cg00121626                   II    19779393
  Color_Channel Random_Loci Methyl27_Loci Is_HMM_Island               NuID
CpGs
1          Both           0             0             0
TIRyS37UTIV_D83QPY    2
2           Red           0             0             1
HarUVHUAFFEvub5ddk    4
3          Both           0             0             0
BY6AMCwUDLLg8vfQ7c    1
4          Both           0             0             0
0Y6CT.7AzG9LP_7oIE    3
5          Both           0             0             0
0IcOoun5CUrHuVxB3Y    5
  Coordinate_37 Chromosome_37 Coordinate_36 Chromosome_36 Genome_Build
enhancer
1       8553009             Y       8613009             Y
37        0
2       9363356             Y       9973356             Y
37        0
3      25314171             Y      23723559             Y
37        0
4      22741795             Y      21151183             Y
37        0
5      21664296             Y      20123684             Y
37        0
  dhs snp snp10 strand gene_body
1   0   0     0      F         0
2   0   0     0      R         1
3   0   0     0      R         1
4   0   1     1      F         1
5   0   0     0      R         1

If you are interested in coincidences of SNP with probes or CpG islands, you
can use GRanges built from these resources.  Others more directly concerned
with these data types can undoubtedly provide more concrete guidance.


On Sun, Aug 14, 2011 at 7:39 AM, khadeeja ismail <hajjja@yahoo.com> wrote:

> Hi All,
>
> I have been going through Biostrings, BSgenome.Hsapiens.UCSC.hg19,
> GenomicRanges
> and SNPlocs.Hsapiens.dbSNP.20101109  to find a way to get the rsIDs of SNPs
> on IlluminaHumanMethylation450k data, and so far unsucessful.
>
> Would be great if anyone could explain how it is done.
>
> Thanks in advance,
>
> Khadeeja
>
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>
>
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