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Submitted SNP(ss) Details: ss12675397           
Submitter
HandleSNP500CANCER
Submitter SNP IDFANCA-02
RefSNP(rs#)rs2239359
Submitted Batch IDSNP500CANCER_07_03_08_A
Submitted DateSep 05, 2008
Publication CitedN.D.
First entry to dbSNPSep 5 2003 12:00:00:000AM
Assay
SpeciesHomo sapiens
Molecular
Type
Genomic
MethodSEQUENCING
Ascertainment Samplesize204
PopulationN.D.
Allele
Observed AlleleA/G
Ancestral AlleleN.D.
Allele OriginT:Germline C:Germline
SNP ClassSNV
CpG CodeN.D.
Validation
Validation StatusbyFreq
HWE Goodness of Fitnot applicable
Variation
Frequency Submissionpopulation count: 10
Genotype Summarypopulation count: 10
Genotype SubmissionN.D.
HaplotypeN.D.

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|ss12675397|allelePos=301|len=601|taxid=9606|alleles='A/G'|mol=Genomic
 TTCACCATGT TAGCCAGGAT GGTCTCCATC TCCTGACCTC RTGATYTGCC CGCCTCAGCC
 TCCCAAAGTG CTGGGATTAC AGGTGTAAGC CGCTGCGCCC GGCTTGTGTT TTAATTTTAC
 TAATGGTTTG CTTTGCATAC TCATAAGTCT GWCTGTAAAG GGCTGTGTTT CTCTACTCAG
 CACTGTGGAT GTTGGAARTG AATTGTGGCC TCCCTGGAGT CCCASGCAGT TCCCWGACTA
 ACGGTGCTGY GCTCTGCTRT CTATCCTCAG GTGCACATTC TCCACCCACC CCTGGTTCCC
 R
 GCAAGTACCG CTCCCTCCTC ACAGACTACA TCTCATTGGC CAAGACACGG CTGGCCGACC
 TCAAGGCAAG CTGTCCCTCC ATGCCCACTC CTCACACCTG TCCCAGCAGA AACTGCTTTG
 TTTTCTTGTT CTCATTCTGT GTMTTCCCTG AAGGTTTCTA TAGAAAACAT GGGACTCTAC
 GAGGATTTGT CATCAGCTGG GGACATTACT GAGGTAATGT TGCTTGAGYC CTGCARGGTC
 TYAGCCAGTC ACGCCCACCA TGCAAAGGTC CAGTTTCTTT TGACTCTTGA GTTGAGTTTT

  Submitted Frequency for ss12675397 back to top

Population ID
 -Class
Sample
(2n)
Major
Allele
Freq.
Minor
Allele
Freq.
Estimated
Heterozygosity
+/-std.err.
Genotype
Freq.
Submitted
Hetero-
zygosity
Submission
Batch
Submitter
CAUC1
MULTI-NATIONAL
62A/G=0.61290300
G/G=0.25806499
A/A=0.12903200
SNP500CANCER_07_03_08_ASNP500CANCER
PAC1
MULTI-NATIONAL
48A/A=0.75000000
A/G=0.20833300
G/G=0.04166700
SNP500CANCER_07_03_08_ASNP500CANCER
HISP1
MULTI-NATIONAL
46A/G=0.47826099
A/A=0.34782600
G/G=0.17391300
SNP500CANCER_07_03_08_ASNP500CANCER
P1
MULTI-NATIONAL
204A/A=0.43137300
A/G=0.42156899
G/G=0.14705899
SNP500CANCER_07_03_08_ASNP500CANCER
AFR1
MULTI-NATIONAL
48A/A=0.58333302
A/G=0.33333299
G/G=0.08333300
SNP500CANCER_07_03_08_ASNP500CANCER
PAC1
MULTI-NATIONAL
48A=0.85399997
G=0.14600000
0.249 +/-0.10208272003SNP500CANCER
CAUC1
MULTI-NATIONAL
62G=0.54799998
A=0.45199999
0.495 +/-0.01708272003SNP500CANCER
AFR1
MULTI-NATIONAL
48A=0.75000000
G=0.25000000
0.375 +/-0.08808272003SNP500CANCER
P1
MULTI-NATIONAL
204A=0.64700001
G=0.35299999
0.457 +/-0.02808272003SNP500CANCER
HISP1
MULTI-NATIONAL
46A=0.58700001
G=0.41299999
0.485 +/-0.03608272003SNP500CANCER
CAUC3
MULTI-NATIONAL
132G/G=0.36363599
A/G=0.34848499
A/A=0.19697000
N/N=0.09090900
SNP500CANCER_07_03_08_BSNP500CANCER
PAC3
MULTI-NATIONAL
178A/G=0.42696601
A/A=0.38202199
G/G=0.15730301
N/N=0.03370800
SNP500CANCER_07_03_08_BSNP500CANCER
P3
MULTI-NATIONAL
560A/A=0.44642901
A/G=0.35357100
G/G=0.15714300
N/N=0.04285700
SNP500CANCER_07_03_08_BSNP500CANCER
AFR3
MULTI-NATIONAL
152A/A=0.57894701
A/G=0.31578901
G/G=0.06578900
N/N=0.03947400
SNP500CANCER_07_03_08_BSNP500CANCER
HISP3
MULTI-NATIONAL
98A/A=0.69387800
A/G=0.28571400
G/G=0.02040800
SNP500CANCER_07_03_08_BSNP500CANCER


  dbSNP summary of Genotypes for ss12675397 back to top

Population ID
 -Class
Total
Sample
(2N)
Founder
(2N)
Major
Allele
Freq.
Minor
Allele
Freq.
Genotype
Freq.
HWE Goodness of FitData
Source
P1
MULTI-NATIONAL
204204A=0.64215684
G=0.35784313A/A=0.43137255
A/G=0.42156863
G/G=0.14705883
Pr(chiSq=0.698,df=1)
=0.439
Genotype
Freq.
CAUC1
MULTI-NATIONAL
6262G=0.56451613
A=0.43548387A/G=0.61290324
G/G=0.25806451
A/A=0.12903225
Pr(chiSq=1.885,df=1)
=0.200
Genotype
Freq.
AFR1
MULTI-NATIONAL
4848A=0.75000000
G=0.25000000A/A=0.58333331
A/G=0.33333334
G/G=0.08333334
Pr(chiSq=0.296,df=1)
=0.655
Genotype
Freq.
HISP1
MULTI-NATIONAL
4646A=0.58695650
G=0.41304347A/G=0.47826087
A/A=0.34782609
G/G=0.17391305
Pr(chiSq=0.004,df=1)
=1.000
Genotype
Freq.
PAC1
MULTI-NATIONAL
4848A=0.85416669
G=0.14583333A/A=0.75000000
A/G=0.20833333
G/G=0.04166667
Pr(chiSq=0.644,df=1)
=0.439
Genotype
Freq.
P3
MULTI-NATIONAL
536536A=0.65111941
G=0.34888059A/A=0.46641791
A/G=0.36940297
G/G=0.16417910
Pr(chiSq=9.364,df=1)
=0.003
Genotype
Freq.
CAUC3
MULTI-NATIONAL
120120G=0.59166664
A=0.40833333G/G=0.40000001
A/G=0.38333333
A/A=0.21666667
Pr(chiSq=2.563,df=1)
=0.150
Genotype
Freq.
AFR3
MULTI-NATIONAL
146146A=0.76712328
G=0.23287672A/A=0.60273975
A/G=0.32876712
G/G=0.06849315
Pr(chiSq=0.465,df=1)
=0.527
Genotype
Freq.
HISP3
MULTI-NATIONAL
9898A=0.83673471
G=0.16326530A/A=0.69387758
A/G=0.28571430
G/G=0.02040816
Pr(chiSq=0.102,df=1)
=0.752
Genotype
Freq.
PAC3
MULTI-NATIONAL
172172A=0.61627907
G=0.38372093A/G=0.44186047
A/A=0.39534885
G/G=0.16279070
Pr(chiSq=0.372,df=1)
=0.584
Genotype
Freq.

  Submitted individual genotype for ss12675397 back to top
There is no individual genotype data for ss12675397.

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