Reference SNP(refSNP) Cluster Report: rs659824

Reference SNP(refSNP) Cluster Report: rs659824

refSNP ID: rs659824
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
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
NM_016938.2:c.728-409T>C
NT_033903.7:g.10942304A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss13609499 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs659824 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
ss832979	SC_JCM\|AP001920.2_68083	rev/B	C/T	aaatgttctgcctgtgaagctcacagttag	tggaggtgaccactgggtgctcaggttgac	07/27/00	10/10/03	83	Genomic	unknown
ss1679987	KWOK\|OVLP-000925-216391	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	10/05/00	10/10/03	87	Genomic	99 %
ss1682002	KWOK\|OVLP-000925-238679	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	10/05/00	10/10/03	87	Genomic	99 %
ss1682391	KWOK\|OVLP-000925-243660	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	10/05/00	10/10/03	87	Genomic	99 %
ss1683883	KWOK\|OVLP-000925-261682	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	10/05/00	10/10/03	87	Genomic	99 %
ss1727389	KWOK\|OVLP-000925-249628	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	10/05/00	10/10/03	87	Genomic	97 %
ss13609499	WI_SSAHASNP\|chr11.NT_033903.6_10809551	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	11/05/03	05/16/04	119	Genomic	unknown
ss16180222	SC_SNP\|NT_033903.6_10809551	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	11/18/03	11/22/03	120	Genomic	unknown
ss16544972	CSHL-HAPMAP\|CSHL-HuAA-200402.chr11.NT_033903.6_10809551	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	02/17/04	03/04/04	120	Genomic	unknown
ss20842509	SSAHASNP\|WGSA-200403-chr11.chr11.NT_033903.6_10809551	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	03/19/04	03/19/04	121	Genomic	unknown
ss24561568	PERLEGEN\|afd1701502	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	08/10/04	09/13/04	123	Genomic	unknown
ss38699706	ABI\|hCV2867125	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	07/16/05	07/16/05	126	Genomic	unknown
ss65836409	KRIBB_YJKIM\|KHS12201	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	10/17/06	12/16/06	127	Genomic	unknown
ss75174393	ILLUMINA\|ILMN_Human_1M_rs659824	fwd/T	A/G	gtcaacctgagcacccagtggtcacctcca	ctaactgtgagcttcacaggcagaacattt	08/28/07	08/29/07	129	Genomic	unknown
ss76748578	AFFY\|AFFY_6_1M_SNP_A-8610102	fwd/T	A/G	ccagtggtcacctcca	ctaactgtgagcttca	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 AGGGTTCAAA GAAAGTTTGC CCAGGCTGCC GCAGCTCACA GACTTCTCTC TGCCCAGAAC
 TGGAAGAAAC ACTAAATAAG TTACTGGGAA TCTAGAGGCT TGGGTGTGAA TCCCACCAGC
 TGATCTAGGG gaatctcatt ttcccaatca gtaaaatgag tgtgttagac tagatgaGTC
 TTATGGGTCT GGCTTGTGCT GTAACGCCCA ATTCCTGCAA CCCACAGTCA ACCTGAGCAC
 CCAGTGGTCA CCTCCA
 R
 CTAACTGTGA GCTTCACAGG CAGAACATTT CCTTTCTCTT GTTCCCCTCA TGCTGCCAGG
 TAGCAGTGAG GCCTCATCCC GCAGCAAAGC ATAACATAGG GGGTACATGC CAGTTTACAG
 GGTGTAAGAA gtctgggatc cagccctggc cccatctcat cctggctgta tgagcttggg
 cgggtcactt aacctctctT AGCTGAATCA TGAAAGTCAC CATTTACCCA GGACTTTGTG
 ATTATTTTTA TGTAATCCTC CCAACAAACG TGGAGGGAGA TATGAATGTC CTCATTTTGT
 AGAGGAAGGA GAAAATCATA CCTCCTAGGA TTCTTGAGAG GAAGGAGGCC AAGTGTGTCA
 GGGAATACAC TACGAGGGCA GGTTCTCATT AAGTGGCAGT TCATTCAC

GeneView

GeneView via analysis of contig annotation: EFEMP2 EGF-containing fibulin-like extracellular matrix protein 2

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_033903->NM_016938

function

HuRef

NW_001838025->NM_016938

function

Celera

NW_925106->NM_016938

function

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


reference	NT_033903->NM_016938->NP_058634	10942304	reverse	intron

HuRef	NW_001838025->NM_016938->NP_058634	3439858	forward	intron

Celera	NW_925106->NM_016938->NP_058634	11308491	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs659824 maps exactly once on NCBI human chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NW_001838025.2	3439858	61963027	minus	C	alt_assembly_8	HuRef	HuRef	view	256
11	NW_925106.1	11308491	62960415	plus	A	alt_assembly_1	Celera	Celera	view	256
11	NT_033903.7	10942304	65393085	plus	A	ref_assembly	reference	reference	view	256

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033903 AP000677 AP000677.3 AP001191 AP001191.2 AP001201 AP001201.5 AP001266 AP001266.2 AP001920.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AP001201.7 AP001266.4	AP000677.3 AP001191.2 AP001920.2

UniGene Cluster ID
381870

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G	N
ss13609499	CEPH		184	AF					0.650	0.350

	HapMap-CEU	European	120	IG	0.267	0.600	0.133	0.100	0.567	0.433

	HapMap-HCB	Asian	90	IG	0.756	0.244		0.371	0.878	0.122

	HapMap-JPT	Asian	88	IG	0.614	0.318	0.068	0.584	0.773	0.227

	HapMap-YRI	Sub-Saharan African	120	IG	0.633	0.333	0.033	0.752	0.800	0.200

	CHMJ	Asian	74	IG					0.784	0.189	0.027

ss24561568	AFD_EUR_PANEL	European	46	IG	0.304	0.304	0.391	0.100	0.457	0.543

	AFD_AFR_PANEL	African American	46	IG	0.348	0.522	0.130	0.655	0.609	0.391

	AFD_CHN_PANEL	Asian	46	IG	0.739	0.261		0.479	0.870	0.130

ss65836409	KHP1		172	AF	0.674	0.314	0.012	0.273	0.831	0.169

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.379+/-0.214	332	260	9	0

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 .