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Platform GPL9704 Query DataSets for GPL9704
Status Public on Dec 03, 2009
Title [GenomeWideSNP_5] Affymetrix Genome-Wide Human SNP 5.0 Chromosome 1
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Homo sapiens
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
 
Description Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

The SNP Array 5.0 is a single microarray featuring all single nucleotide polymorphisms (SNPs) from the original two-chip Mapping 500K Array Set, as well as 420,000 additional non-polymorphic probes that can measure other genetic differences, such as copy number variation.
SNPs on the array are present on 200 to 1,100 base pair (bp) Nsp I or Sty I digested fragments in the human genome, and are amplified using the fifth generation of the Whole-genome Sampling Assay (WGSA).

Contains SNPs on NC_000001.9
Annotations correspond to hg18 (NCBI 36.1)
 
Submission date Nov 20, 2009
Last update date May 25, 2012
Contact name Christina Curtis
E-mail(s) christina.curtis@cancer.org.uk
Phone 01223404231
Fax 1223 404208
Organization name University of Cambridge
Department Computational Biology/Oncology
Lab Tavaré
Street address Robinson Way
City Cambridge
ZIP/Postal code CB20RE
Country United Kingdom
 
Samples (50) GSM474135, GSM474136, GSM474137, GSM474138, GSM474139, GSM474140 
Series (1)
GSE16400 The pitfalls of platform comparison: DNA copy number array technologies assessed
Relations
Affiliated with GPL6804

Data table header descriptions
ID Unique identifier for the SNP or CNV probe set
Chromosome Chromosome (1-22, X, Y)
RANGE_GB NCBI RefSeq Accession for chromosome (hg18, 36.1)
RANGE_START The start base position of the 5'-most probe in the probe set.
RANGE_STOP The end base position of the 3'-most probe in the probe set.
STRAND The strand (of the reference genome) where the CN probe set or SNP maps.
Physical Position
dbSNP RS ID SNP identifier from dbSNP
Allele A
Allele B
SPOT_ID

Data table
ID Chromosome RANGE_GB RANGE_START RANGE_STOP STRAND Physical Position dbSNP RS ID Allele A Allele B SPOT_ID
SNP_A-1780654 1 NC_000001.9 - 21039991 rs7553394 C T
SNP_A-1785311 1 NC_000001.9 - 206077697 rs947658 A G
SNP_A-1785727 1 NC_000001.9 - 94865998 rs17111912 A G
SNP_A-4192955 1 NC_000001.9 + 180026280 rs704326 A G
SNP_A-1787624 1 NC_000001.9 - 246005371 rs6587481 A G
SNP_A-1789472 1 NC_000001.9 - 2442429 rs2985862 A G
SNP_A-1789739 1 NC_000001.9 + 206194996 rs11579772 A G
SNP_A-1791691 1 NC_000001.9 - 180252338 rs12564637 C T
SNP_A-1795691 1 NC_000001.9 - 117967619 rs2884587 A G
SNP_A-1796596 1 NC_000001.9 + 68053839 rs17130314 G T
SNP_A-4193854 1 NC_000001.9 + 156673544 rs12119297 C T
SNP_A-4194375 1 NC_000001.9 + 12777117 rs1063776 C G
SNP_A-4194530 1 NC_000001.9 + 207855326 rs10746422 C T
SNP_A-1807592 1 NC_000001.9 + 154836390 rs16837540 C T
SNP_A-1810126 1 NC_000001.9 + 87703477 rs6683030 C T
SNP_A-4195243 1 NC_000001.9 - 214658626 rs4253963 A G
SNP_A-1818131 1 NC_000001.9 + 180227828 rs11800037 A G
SNP_A-4195660 1 NC_000001.9 + 224621925 rs1136410 A G
SNP_A-4195809 1 NC_000001.9 + 227689961 rs1065674 C T
SNP_A-1823250 1 NC_000001.9 - 180178383 rs2485925 A G

Total number of rows: 62850

Table truncated, full table size 3244 Kbytes.




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Supplementary data files not provided
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