Reference SNP(refSNP) Cluster Report: rs352227

Reference SNP(refSNP) Cluster Report: rs352227

refSNP ID: rs352227
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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_017412.2:c.1405-424T>C
NT_023666.17:g.6782983T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1921150 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs352227 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
ss447505	KWOK\|OVLP-000621-368874	rev/T	A/G	atttgatgttttcatttataaggttttata	gtaattttcttatgtggaaaaaatatactc	06/30/00	10/10/03	79	Genomic	99 %
ss447756	KWOK\|OVLP-000621-369496	fwd/B	C/T	gagtatattttttccacataagaaaattac	tataaaaccttataaatgaaaacatcaaat	06/30/00	10/10/03	85	Genomic	99 %
ss590546	SC_JCM\|AC013829.4_109963	fwd/B	C/T	gagtatattttttccacataagaaaattac	tataaaaccttataaatgaaaacatcaaat	07/12/00	10/10/03	87	Genomic	unknown
ss920744	KWOK\|OVLP-000804-243002	rev/T	A/G	atttgatgttttcatttataaggttttata	gtaattttcttatgtggaaaaaatatactc	09/01/00	10/10/03	86	Genomic	99 %
ss921141	KWOK\|OVLP-000804-245867	fwd/B	C/T	gagtatattttttccacataagaaaattac	tataaaaccttataaatgaaaacatcaaat	09/01/00	10/10/03	86	Genomic	99 %
ss1921150	KWOK\|OVLP-000925-614092	rev/T	A/G	atttgatgttttcatttataaggttttata	gtaattttcttatgtggaaaaaatatactc	10/06/00	10/25/06	87	Genomic	99 %
ss1921439	KWOK\|OVLP-000925-616115	fwd/B	C/T	gagtatattttttccacataagaaaattac	tataaaaccttataaatgaaaacatcaaat	10/06/00	10/10/03	87	Genomic	99 %
ss14349617	WI_SSAHASNP\|chr8.NT_023666.16_6782983	fwd/B	C/T	gagtatattttttccacataagaaaattac	tataaaaccttataaatgaaaacatcaaat	11/05/03	11/22/03	119	Genomic	unknown
ss22740343	SSAHASNP\|WGSA-200403-chr8.chr8.NT_023666.16_6782983	fwd/B	C/T	gagtatattttttccacataagaaaattac	tataaaaccttataaatgaaaacatcaaat	03/21/04	03/21/04	121	Genomic	unknown
ss43264545	ABI\|hCV1018328	fwd/B	C/T	gagtatattttttccacataagaaaattac	tataaaaccttataaatgaaaacatcaaat	07/18/05	07/18/05	126	Genomic	unknown
ss81797837	HGSV\|Cor18555_SNV_20070510.chr8_28464615	fwd/B	C/T	gagtatattttttccacataagaaaattac	tataaaaccttataaatgaaaacatcaaat	11/27/07	12/01/07	130	Genomic	unknown
ss84587387	HGSV\|Cor19129_SNV_20070510.chr8_28464615	fwd/B	C/T	gagtatattttttccacataagaaaattac	tataaaaccttataaatgaaaacatcaaat	12/06/07	12/07/07	130	Genomic	unknown

Fasta sequence (Legend)

 TTTTCACATT ACTCTTTTAA GAAGTTCATC TACATCACCA CTGCCTCTCT CCCGCCATTG
 TACAAATGCT GTCCATTCTT CCCTATTTTA GAAGATGACT AATGTCAGCC AAATATCTAT
 CATCTATCta gatagataga tagatagata TGGCTCAATG TATAGAGTAT AAATTTATTG
 CCAAATTTTC AGGAGTATAT TTTTTCCACA TAAGAAAATT AC
 Y
 TATAAAACCT TATAAATGAA AACATCAAAT TTGTAGAATT ATTTTACTCT ATTTTATTTA
 AAAGATTTTG ggccaggcgc agtggctcac gcctgtaatc ccagcacttt gggaggctga
 ggcaggtgga tcacctgcag cctggccaac atggtgaaac cccgtctcta ctaaaaatac
 aaaaattacc tgggcatatt ggcatatacc tgtaatccta gctacttggg aggctgtgag
 gcaggagaat tgcttgaacc tgggaggcag aggttgcagt gagccaagat cacaccattg
 cactccagcc tgggtgacaa gaacaaaact ctgtctcaaa agaaaaagaa aaaGATTTCA
 TAATGGCCTT TAATAGAAAG TTATTTTTAT ATATTTAAGA TGCTTTTCTT TCTGTTCTTC
 CAGGTTACTC AAATGAGTCG TCCAGACTTG ATTCTCTTTC TGATGAAATA CCTGATGGCT
 CTC

GeneView

GeneView via analysis of contig annotation: FZD3 frizzled homolog 3 (Drosophila)

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_023666->NM_017412

function

HuRef

NW_001839127->NM_017412

function

Celera

NW_923907->NM_017412

function

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


reference	NT_023666->NM_017412->NP_059108	6782983	forward	intron

HuRef	NW_001839127->NM_017412->NP_059108	6786920	forward	intron

Celera	NW_923907->NM_017412->NP_059108	15936350	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs352227 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_001839127.1	6786920	26953819	plus	C	alt_assembly_8	HuRef	HuRef	view	222
8	NW_923907.1	15936350	27368512	plus	C	alt_assembly_1	Celera	Celera	view	222
8	NT_023666.17	6782983	28464615	plus	T	ref_assembly	reference	reference	view	222

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023666 AC012411 AC012411.3 AC013829.4

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC011132.15 AC013829.13 NC_000008.9	AC012411.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1921150	HapMap-CEU	European	106	IG	0.415	0.472	0.113	1.000	0.651	0.349

	HapMap-HCB	Asian	84	IG	0.476	0.524		0.025	0.738	0.262

	HapMap-JPT	Asian	86	IG	0.279	0.465	0.256		0.512	0.488

	HapMap-YRI	Sub-Saharan African	116	IG	0.603	0.293	0.103	0.100	0.750	0.250

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.443+/-0.159	270	210	0	0

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

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Revised: May 25, 2006 1:38 PM .