Reference SNP(refSNP) Cluster Report: rs799916

Reference SNP(refSNP) Cluster Report: rs799916

refSNP ID: rs799916
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3
Citation:	PubMed

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/C
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NG_005905.1:g.44789A>C
NM_007294.2:c.4097-141A>C
NM_007295.2:c.4097-141A>C
NM_007296.2:c.4097-141A>C
NM_007297.2:c.3209-141A>C
NM_007298.2:c.548-141A>C
NM_007299.2:c.4097-141A>C
NM_007300.2:c.4097-141A>C
NM_007302.2:c.3974-141A>C
NM_007303.2:c.671-141A>C
NM_007304.2:c.788-141A>C
NM_007305.2:c.665-141A>C
NT_010755.15:g.4967486T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44038065 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs799916 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss1005845	KWOK\|OVLP-000804-134710	rev/B	G/T	aaatgattaaattccttgctttgggacacc	ggatttgcttttataaaatgaaaccagaag	09/02/00	10/10/03	86	Genomic	97 %
ss1638870	KWOK\|OVLP-000925-356002	rev/B	G/T	aaatgattaaattccttgctttgggacacc	ggatttgcttttataaaatgaaaccagaag	10/04/00	10/10/03	87	Genomic	97 %
ss2659978	SC_JCM\|L78833.1_37559	fwd/T	A/C	cttctggtttcattttataaaagcaaatcc	ggtgtcccaaagcaaggaatttaatcattt	11/03/00	10/10/03	89	Genomic	unknown
ss2984209	YUSUKE\|IMS-JST005853	fwd/T	A/C	cttctggtttcattttataaaagcaaatcc	ggtgtcccaaagcaaggaatttaatcattt	05/24/01	10/10/03	96	Genomic	unknown
ss8486263	EGP_SNPS\|BRCA1-035166	fwd/T	A/C	cttctggtttcattttataaaagcaaatcc	ggtgtcccaaagcaaggaatttaatcattt	04/22/03	04/07/04	117	Genomic	unknown
ss12415913	WI_SSAHASNP\|chr17.NT_010755.13_4965913	rev/B	G/T	aaatgattaaattccttgctttgggacacc	ggatttgcttttataaaatgaaaccagaag	07/04/03	10/10/03	116	Genomic	unknown
ss21381988	SSAHASNP\|WGSA-200403-chr17.chr17.NT_010755.14_4965688	rev/B	G/T	aaatgattaaattccttgctttgggacacc	ggatttgcttttataaaatgaaaccagaag	03/19/04	03/19/04	121	Genomic	unknown
ss24588203	PERLEGEN\|afd0820057	rev/B	G/T	aaatgattaaattccttgctttgggacacc	ggatttgcttttataaaatgaaaccagaag	08/10/04	09/13/04	123	Genomic	unknown
ss44038065	ABI\|hCV7530109	rev/B	G/T	aaatgattaaattccttgctttgggacacc	ggatttgcttttataaaatgaaaccagaag	07/18/05	11/03/06	126	Genomic	unknown
ss66465481	AFFY\|SNP_A-2254720	rev/B	G/T	cttgctttgggacacc	ggatttgcttttataa	10/29/06	08/14/07	127	Genomic	unknown
ss66863054	EGP_SNPS\|BRCA1_035166	fwd/T	A/C	cttctggtttcattttataaaagcaaatcc	ggtgtcccaaagcaaggaatttaatcattt	11/09/06	08/14/07	127	Genomic	unknown
ss75214623	ILLUMINA\|ILMN_Human_1M_rs799916	fwd/T	A/C	cttctggtttcattttataaaagcaaatcc	ggtgtcccaaagcaaggaatttaatcattt	08/28/07	08/29/07	129	Genomic	unknown
ss76268267	AFFY\|AFFY_6_1M_SNP_A-2254720	rev/B	G/T	cttgctttgggacacc	ggatttgcttttataa	08/28/07	08/30/07	129	Genomic	unknown
ss78615622	HGSV\|Cor12878_SNV_20070510.chr17_38496716	rev/B	G/T	aaatgattaaattccttgctttgggacacc	ggatttgcttttataaaatgaaaccagaag	10/17/07	10/20/07	129	Genomic	unknown

Fasta sequence (Legend)

 AAAATAATCA AGAAGAGCAA AGCATGGATT CAAACTTAGG TATTGGAACC AGGTTTTTGT
 GTTTGCCCCA GTCTATTTAT AGAAGTGAGC TAAATGTTTA TGCTTTTGGG GAGCACATTT
 TACAAATTTC CAAGTATAGT TAAAGGAACT GCTTCTTAAA CTTGAAACAT GTTCCTCCTA
 AGGTGCTTTT CATAGAAAAA AGTCCTTCAC ACAGCTAGGA CGTCATCTTT GACTGAATGA
 GCTTTAACAT CCTAATTACT GGTGGACTTA CTTCTGGTTT CATTTTATAA AAGCAAATCC
 M
 GGTGTCCCAA AGCAAGGAAT TTAATCATTT TGTGTGACAT GAAAGTAAAT CCAGTCCTGC
 CAATGAGAAG AAAAAGACAC AGCAAGTTGC AGCGTTTATA GTCTGCTTTT ACATCTGAAC
 CTCTGTTTTT GTTATTTAAG GTGAAGCAGC ATCTGGGTGT GAGAGTGAAA CAAGCGTCTC
 TGAAGACTGC TCAGGGCTAT CCTCTCAGAG TGACATTTTA ACCACTCAGG TAAAAAGCGT
 GTGTGTGTGT GCACATGCGT GTGTGTGGTG TCCTTTGCAT TCAGTAGTAT GTATCCCACA

GeneView

GeneView via analysis of contig annotation: BRCA1 breast cancer 1, early onset

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_010755->NM_007294

function

reference

NT_010755->NM_007295

function

reference

NT_010755->NM_007296

function

reference

NT_010755->NM_007297

function

reference

NT_010755->NM_007298

function

reference

NT_010755->NM_007299

function

reference

NT_010755->NM_007300

function

reference

NT_010755->NM_007302

function

reference

NT_010755->NM_007303

function

reference

NT_010755->NM_007304

function

reference

NT_010755->NM_007305

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_010755->NM_007294->NP_009225	4967486	reverse	intron

reference	NT_010755->NM_007295->NP_009226	4967486	reverse	intron

reference	NT_010755->NM_007296->NP_009227	4967486	reverse	intron

reference	NT_010755->NM_007297->NP_009228	4967486	reverse	intron

reference	NT_010755->NM_007298->NP_009229	4967486	reverse	intron

reference	NT_010755->NM_007299->NP_009230	4967486	reverse	intron

reference	NT_010755->NM_007300->NP_009231	4967486	reverse	intron

reference	NT_010755->NM_007302->NP_009233	4967486	reverse	intron

reference	NT_010755->NM_007303->NP_009234	4967486	reverse	intron

reference	NT_010755->NM_007304->NP_009235	4967486	reverse	intron

reference	NT_010755->NM_007305->NP_009236	4967486	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs799916 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838436.2	154219	37009506	plus	C	alt_assembly_8	HuRef	HuRef	view	300
17	NW_926828.1	4771245	37900054	minus	G	alt_assembly_1	Celera	Celera	view	300
17	NT_010755.15	4967486	38496716	minus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010755 AC060780 L78833.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss24588203	AFD_EUR_PANEL	European	48	IG	0.375	0.458	0.167	1.000	0.604	0.396

	AFD_AFR_PANEL	African American	44	IG	0.091	0.318	0.591	0.479	0.250	0.750

	AFD_CHN_PANEL	Asian	48	IG	0.292	0.625	0.083	0.150	0.604	0.396

ss44038065	HapMap-CEU	European	120	IG	0.417	0.450	0.133		0.642	0.358

	HapMap-HCB	Asian	90	IG	0.467	0.444	0.089		0.689	0.311

	HapMap-JPT	Asian	90	IG	0.511	0.422	0.067		0.722	0.278

	HapMap-YRI	Sub-Saharan African	120	IG	0.067	0.267	0.667		0.200	0.800

	AoD_African_American		90	AF					0.270	0.730

	AoD_Caucasian		92	AF					0.700	0.300

ss66465481	HapMap-CEU	European	118	GF	0.424	0.458	0.119		0.653	0.347

	HapMap-HCB	Asian	90	GF	0.467	0.444	0.089		0.689	0.311

	HapMap-JPT	Asian	90	GF	0.511	0.422	0.067		0.722	0.278

	HapMap-YRI	Sub-Saharan African	120	GF	0.067	0.267	0.667		0.200	0.800

ss66863054	HSP_GENO_PANEL		120	IG	0.350	0.467	0.183	1.000	0.583	0.417

	CEU_GENO_PANEL	European	120	IG	0.417	0.450	0.133	1.000	0.642	0.358

	AAM_GENO_PANEL	African American	124	IG	0.129	0.403	0.468	0.527	0.331	0.669

	CHB_GENO_PANEL	Asian	90	IG	0.467	0.444	0.089	1.000	0.689	0.311

	YRI_GENO_PANEL	Sub-Saharan African	120	IG	0.067	0.267	0.667	0.200	0.200	0.800

	JPT_GENO_PANEL	Asian	90	IG	0.489	0.444	0.067	0.584	0.711	0.289

ss8486263	PDR90	Global	150	IG	0.360	0.373	0.267	0.050	0.547	0.453

	CEPH		184	AF					0.560	0.440

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict	Additional Freq. Data
	0.499+/-0.027	545	473	270	0	ALFRED: The Allele Frequency Database

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

YES

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Revised: May 25, 2006 1:38 PM .