Submitted SNP(ss) Details: ss5586200

Submitted SNP(ss) Details: ss5586200

Submitter
Handle	SNP500CANCER
Submitter SNP ID	PARP1-08
RefSNP(rs#)	rs1805408
Submitted Batch ID	08272003_update
Submitted Date	Oct 28, 2003
Publication Cited	N.D.
First entry to dbSNP	Sep 26 2002 12:00:00:000AM

Resource Links
GenBank Accession	NT_004525.13
Submitted Gene Name	N.D
Submitted Gene ID	N.D.
Submitted SNP Synonyms	N.D
Submitted linkout	PARP1-08

Assay
Species	Homo sapiens
Molecular Type	Genomic
Method	SEQUENCING
Ascertainment Samplesize	204
Population	P1

Allele
Observed Allele	A/G
Ancestral Allele	N.D.
Allele Origin	N/A
SNP Class	SNV
CpG Code	c_g/a

Validation
Validation Status
HWE Goodness of Fit	not applicable

Variation
Frequency Submission	population count: 5
Genotype Summary	population count: 19
Genotype Submission	N.D.
Haplotype	N.D.

Comment
Platform: Sequencing Primer F: TCTGGTAAACAGGATGACGC, Temp: 50, GC Content:50, Product Size: 365 Primer R: TGTAGTCCCGCATTTGCC, Temp: 51.6, GC Content:55.56 Platform: TaqMan Forward primer: CTGACGTGTTTCTC, Amount: 900 nM Reverse primer: GAAGGAGGGCACCGAACAC, Amount: 900 nM Probe 1: TCTGACATGTTTCTC, Amount: 200 nM Probe 2: TTTTTGTAGTCCCGCATTTGC, Amount: 200 nM Annealing temperature: 60 C

Fasta sequence (Legend)

 GGGGGCGCTG CAGGAACACT TGGAAATAAG GTCTCCTACA AGAATCCAAG CTCCATTGTA
 AACCAAGGGT GGGTGGGGTG TTAAGAGCCC CATAGCAAGC CCACAGCAAG AAGCCTCTCT
 TCTTTGTAGT GAGTGGAATC TGTGCAAGTT CCTCCATCCC ACATTAGTAA GTGTCCTTTT
 TTGTAGTCCC GCATTTGCCC TCTGAC
 R
 TGTTTCTCCA CTGGCTGCAG ATCTTGGACC GAGTAGCYGA TGGCATGGTG TTCGGTGCCC
 TCCTTCCCTG CGAGGAATGC TCGGGTCAGC TGGTCTTCAA GAGCGATGCC TATTACTGCA
 CTGGGGACGT CACTGCCTGG ACCAAGTGTA TGGTCAAGAC ACAGACACCC AACCGGAAGG
 AGTGGRTAAC CCCAAAGGTA AGGGGTAGGG GAAGATCCTG GGATCTGTTG GGAGAAAAAC
 CTGGCCCCAC TTTCTGCGCT TGTTTATACT TCAGGTCCCT GAGATTGCAG GGCCATGTTC
 CTCAGA

Submitted Frequency for ss5586200

Population ID -Class	Sample (2n)	Major Allele Freq.	Minor Allele Freq.	Estimated Heterozygosity +/-std.err.	Genotype Freq.	Submitted Hetero- zygosity	Submission Batch	Submitter
PAC1 - MULTI-NATIONAL	48	A=0.68800002	G=0.31200001	0.429 +/-0.071	A/A=0.54200000 A/G=0.29200000 G/G=0.16599999	0.292	08272003	SNP500CANCER
P1 - MULTI-NATIONAL	204	A=0.77899998	G=0.22100000	0.344 +/-0.046	A/A=0.62699997 A/G=0.30399999 G/G=0.06900000	0.304	08272003	SNP500CANCER
CAUC1 - MULTI-NATIONAL	62	A=0.90300000	G=0.09700000	0.175 +/-0.086	A/A=0.80599999 A/G=0.19400001 G/G=0.00000000	0.194	08272003	SNP500CANCER
AFR1 - MULTI-NATIONAL	48	A=0.64600003	G=0.35400000	0.457 +/-0.057	A/G=0.45800000 A/A=0.41700000 G/G=0.12500000	0.458	08272003	SNP500CANCER
HISP1 - MULTI-NATIONAL	46	A=0.84799999	G=0.15200000	0.258 +/-0.104	A/A=0.69599998 A/G=0.30399999 G/G=0.00000000	0.304	08272003	SNP500CANCER

dbSNP summary of Genotypes for ss5586200

Population ID -Class	Total Sample (2N)	Founder (2N)	Major Allele Freq.	Minor Allele Freq.	Genotype Freq.	HWE Goodness of Fit	Data Source
HAPMAP-CHB	82	82	A=0.73170733	G=0.26829270	A/A=0.60975611 A/G=0.24390244 G/G=0.14634146	Pr(chiSq=5.883,df=1) =0.020	Genotype Freq.
HapMap-HCB - EAST ASIA	86	86	A=0.69767439	G=0.30232558	A/A=0.51162791 A/G=0.37209302 G/G=0.11627907	Pr(chiSq=0.598,df=1) =0.479	Genotype Freq.
HAPMAP-ASW	98	98	A=0.64285713	G=0.35714287	A/G=0.42857143 A/A=0.42857143 G/G=0.14285715	Pr(chiSq=0.218,df=1) =0.655	Genotype Freq.
HAPMAP-MEX	100	100	A=0.86000001	G=0.14000000	A/A=0.74000001 A/G=0.23999999 G/G=0.02000000	Pr(chiSq=0.001,df=1) =1.000	Genotype Freq.
HAPMAP-CHD	170	170	A=0.67058825	G=0.32941177	A/A=0.45882353 A/G=0.42352942 G/G=0.11764706	Pr(chiSq=0.145,df=1) =0.752	Genotype Freq.
HapMap-JPT	172	172	A=0.75000000	G=0.25000000	A/A=0.55813956 A/G=0.38372093 G/G=0.05813954	Pr(chiSq=0.047,df=1) =1.000	Genotype Freq.
HAPMAP-GIH	176	176	A=0.78977275	G=0.21022727	A/A=0.63636363 A/G=0.30681819 G/G=0.05681818	Pr(chiSq=0.509,df=1) =0.479	Genotype Freq.
HAPMAP-TSI	176	176	A=0.82954544	G=0.17045455	A/A=0.65909094 A/G=0.34090909	Pr(chiSq=1.159,df=1) =0.294	Genotype Freq.
HAPMAP-LWK	180	180	A=0.57222223	G=0.42777777	A/G=0.45555556 A/A=0.34444445 G/G=0.20000000	Pr(chiSq=0.434,df=1) =0.527	Genotype Freq.
HapMap-CEU	224	224	A=0.78571427	G=0.21428572	A/A=0.62500000 A/G=0.32142857 G/G=0.05357143	Pr(chiSq=0.231,df=1) =0.655	Genotype Freq.
HapMap-YRI	226	226	A=0.57964599	G=0.42035398	A/G=0.48672566 A/A=0.33628318 G/G=0.17699115	Pr(chiSq=0.000,df=1) =1.000	Genotype Freq.
HAPMAP-MKK	276	276	A=0.74637681	G=0.25362319	A/A=0.57246375 A/G=0.34782609 G/G=0.07971015	Pr(chiSq=0.912,df=1) =0.343	Genotype Freq.

Submitted individual genotype for ss5586200

There is no individual genotype data for ss5586200.

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