Reference SNP(refSNP) Cluster Report: rs341704

Reference SNP(refSNP) Cluster Report: rs341704

refSNP ID: rs341704
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

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

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44875446 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs341704 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
ss435243	KWOK\|OVLP-000621-338463	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	06/30/00	10/10/03	79	Genomic	99 %
ss792198	SC_JCM\|AC023296.2_107024	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	07/27/00	10/10/03	85	Genomic	unknown
ss1081522	KWOK\|OVLP-000804-73126	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	09/02/00	10/10/03	86	Genomic	99 %
ss1934039	KWOK\|OVLP-000925-726528	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	10/06/00	10/10/03	87	Genomic	99 %
ss3101848	TSC-CSHL\|TSC1202991	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	06/07/01	10/25/06	96	Genomic	unknown
ss5207862	TSC-CSHL\|TSC1215605	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	09/20/02	10/10/03	108	Genomic	unknown
ss5877951	SC_JCM\|NT_023744.10_840007	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	01/10/03	10/10/03	111	Genomic	unknown
ss22678144	SSAHASNP\|WGSA-200403-chr8.chr8.NT_023736.16_2733280	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	03/21/04	03/21/04	121	Genomic	unknown
ss24692669	PERLEGEN\|afd1844414	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	08/10/04	09/13/04	123	Genomic	unknown
ss44875446	ABI\|hCV1513365	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	07/19/05	11/03/06	126	Genomic	unknown
ss66746142	ILLUMINA\|HumanHap300v1.1_rs341704	fwd/B	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	11/09/06	11/09/06	127	Genomic	unknown
ss67294928	ILLUMINA\|HumanHap550v1.1_rs341704	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	11/14/06	11/14/06	127	Genomic	unknown
ss67699052	ILLUMINA\|HumanHap650Yv1.0_rs341704	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	11/14/06	11/14/06	127	Genomic	unknown
ss69035396	PERLEGEN\|PGP01844414	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	01/30/07	08/14/07	127	Genomic	unknown
ss70773543	ILLUMINA\|HumanHap550v3.0__rs341704	rev/B	C/T	gttcaaagagaatgctttccaacactctca	gtgaacaaatctaatccctttattgataag	04/20/07	03/30/08	130	Genomic	unknown
ss71349208	ILLUMINA\|HumanHap650Yv3.0_rs341704	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	04/23/07	04/23/07	127	Genomic	unknown
ss75692187	ILLUMINA\|ILMN_Human_1M_rs341704	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	08/28/07	08/29/07	129	Genomic	unknown
ss79161482	ILLUMINA\|HumanHap300v2.0_rs341704	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	04/18/07	11/18/07	130	Genomic	unknown
ss83432990	KRIBB_YJKIM\|KHS460434	fwd/T	A/G	cttatcaataaagggattagatttgttcac	tgagagtgttggaaagcattctctttgaac	12/04/07	12/05/07	130	Genomic	unknown

Fasta sequence (Legend)

 ACTATATATA TATTTTTATT GCAGTAAGAT TATTGTTATG GCCATATTGT TCGGATTGTT
 GCCTGTCCTA AAGAAAATAA TACATTATAA TGATAAATAT ATAAATATAA TATAAATACG
 TACATACAGG TAGCGATTGC TAAATAGATA TTTTGTACTA TTTGCTGTAG TGAAGGGATC
 ACAAAACAGA AGGAAGCCAA TTTGTATGTT CTCCAATTCT AATGATGTGA CTTTAGACAT
 TTGAAAAATG CCTCTCTGGG CCTTATTTAC CTTATCAATA AAGGGATTAG ATTTGTTCAC
 R
 TGAGAGTGTT GGAAAGCATT CTCTTTGAAC ACCAGCCCTA TGGGGTATTC TCAACATAAA
 GAATGACATT GTCTTCTCCA TTTGGGCATT GCTGCAAATT ACATCCCCCG CATGGAAAGG
 TACACGCCTG TTGAGGCAGT GAAGACTCTT CTCCATTTGG GCATTGCTGG AAATTACATC
 CCCTGCATGG AAAGGTACAT GCCTGTTGAG GCAGTGAAGA CTCTTCTCCA TTTGGGGATT
 GCTGGAAATT ACATCCCCCG CATGGAAAGG TACACGCCTG TTGAGGCAGT GAAGACTCTT

GeneView

GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs341704 maps exactly once on NCBI human chromosome 8

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
8	NW_001839109.2	4309041	2529669	minus	C	alt_assembly_8	HuRef	HuRef	view	300
8	NW_923840.1	539173	2720270	plus	A	alt_assembly_1	Celera	Celera	view	300
8	NT_023736.16	2733280	2733280	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023744.10 AC023296.2 AC055749

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24692669	AFD_EUR_PANEL	European	46	IG	0.261	0.522	0.217	1.000	0.522	0.478

	AFD_AFR_PANEL	African American	46	IG	0.043	0.478	0.478	0.403	0.283	0.717

	AFD_CHN_PANEL	Asian	48	IG	0.500	0.333	0.167	0.251	0.667	0.333

ss44875446	HapMap-CEU	European	120	IG	0.233	0.500	0.267	1.000	0.483	0.517

	HapMap-HCB	Asian	90	IG	0.422	0.422	0.156	0.584	0.633	0.367

	HapMap-JPT	Asian	90	IG	0.556	0.422	0.022	0.251	0.767	0.233

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.467	0.450	0.584	0.317	0.683

ss69035396	HapMap-CEU	European	120	GF	0.233	0.483	0.283		0.475	0.525

	HapMap-HCB	Asian	90	GF	0.422	0.400	0.178		0.622	0.378

	HapMap-JPT	Asian	90	GF	0.556	0.422	0.022		0.767	0.233

	HapMap-YRI	Sub-Saharan African	120	GF	0.083	0.450	0.467		0.308	0.692

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss24692669	71	19	31	20
ss44875446	266	73	123	70
ss69035396	266	73	123	70

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs341704	332	88	151	89

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
239	ss44875446	A/G	CSHL-HAPMAP	HapMap-CEU	NA11882	CEPH1347.15	r23_ch8_CEU_illumina:infinium_genotyping_2.0.0	672074
239	ss69035396	G/G	CSHL-HAPMAP	HapMap-CEU	NA11882	CEPH1347.15	chr8-HapMap-CEU
456	ss44875446	A/A	CSHL-HAPMAP	HapMap-CEU	NA10838	CEPH1420.01	r23_ch8_CEU_illumina:infinium_genotyping_2.0.0	672074
456	ss69035396	A/G	CSHL-HAPMAP	HapMap-CEU	NA10838	CEPH1420.01	chr8-HapMap-CEU
5187	ss44875446	A/G	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	r23_ch8_HCB_illumina:infinium_genotyping_2.0.0	672074
5187	ss69035396	G/G	CSHL-HAPMAP	HapMap-HCB	NA18633	CH18633	chr8-HapMap-HCB
5261	ss44875446	A/G	CSHL-HAPMAP	HapMap-YRI	NA18856	YOR023.03	r23_ch8_YRI_illumina:infinium_genotyping_2.0.0	672074
5261	ss69035396	G/G	CSHL-HAPMAP	HapMap-YRI	NA18856	YOR023.03	chr8-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .