Reference SNP(refSNP) Cluster Report: rs612783

Reference SNP(refSNP) Cluster Report: rs612783

refSNP ID: rs612783
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:	A
Clinical Association:	unknown

HGVS Names
NM_001792.2:c.173-29192A>G
NT_010966.13:g.7112167T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1783346 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs612783 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
ss784995	SC_JCM\|AC015933.5_134974	fwd/T	A/G	ttgttccgttttatgactgagtagtattcc	tggtgtatatatatatcacagccaacaaat	07/27/00	10/10/03	83	Genomic	unknown
ss1783346	KWOK\|OVLP-000925-405470	fwd/T	A/G	ttgttccgttttatgactgagtagtattcc	tggtgtatatatatatcacagccaacaaat	10/05/00	10/25/06	94	Genomic	99 %
ss2832339	TSC-CSHL\|TSC1011303	fwd/T	A/G	ttgttccgttttatgactgagtagtattcc	tggtgtatatatatatcacagccaacaaat	01/03/01	10/10/03	92	Genomic	unknown
ss40938186	ABI\|hCV26131957	rev/B	C/T	atttgttggctgtgatatatatatacacca	ggaatactactcagtcataaaacggaacaa	07/17/05	07/17/05	126	Genomic	unknown

Fasta sequence (Legend)

 AACTCAGAAT GAGACTTTTC AAAGAGGATG ATAATAAGAA TAGTGCTGGT GGGGAATTTA
 TTTCAAGAGG AAAAACCATA AAGTTTGGAG TGAAATTAGA TGTAATGGAA GAAAACTCAG
 TGCCATCAGC CACTAGGGGT CTAGTTTAAG TGTCCTTAAA GCTCATAAGT CCCCATCAAC
 TACTTCAAAT CAAACCTGTT tatatatata tatatatata tttatatata tatatatata
 tatatatata tatatttatt tatatcagta atttttaggg tacaggtggt ttttggttat
 atggataagt tctttagtag tgatttctga gattttggtg tacctgtcac ccaagcagtg
 tacactgtac ccagtgtgta accttttatc cttcacccgc ctcccaccct tccccgtgag
 tccccaaagt ccattatatt aatattattc ttatgccttt gtatcctcat agcttagctc
 ccgcttataa gtgagaacat atgatatttg gttttctatt cctgagttac ctcacttaga
 ataatggcct ccagctccat ccaagttgct gcaaaggcca ttattttgtt ccgttttatg
 actgagtagt attcc
 R
 tggtgtatat atatatcaca GCCAACAAAT AGTTGATTTC TTTTTAACTA TATGCTGATG
 ATAATTCTTG CTTTAATATT GGCAACAACT GACTGGCAGT GCCAGAAACA GAAGCAAATC
 TCTTCTTGAC TGATTGAATA CAAATAAAAT TTGCAAATAG TTTTTATTAT GATCCATATC
 TTCGATTTTC AAATATCAAC ATTATGTTTC CTTAGTAGGA

GeneView

GeneView via analysis of contig annotation: CDH2 cadherin 2, type 1, N-cadherin (neuronal)

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_010966->NM_001792

function

Celera

NW_927095->NM_001792

function

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


reference	NT_010966->NM_001792->NP_001783	7112167	reverse	intron

Celera	NW_927095->NM_001792->NP_001783	7102880	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs612783 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_927095.1	7102880	22434475	minus	T	alt_assembly_1	Celera	Celera	view	615
18	NW_001838467.2	18925588	22475214	plus	A	alt_assembly_8	HuRef	HuRef	view	615
18	NT_010966.13	7112167	23877063	minus	T	ref_assembly	reference	reference	view	615

NCBI Resource Links

Submitter-Referenced
GenBank
AC015933.5 AP001105.3 AP001145

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC015933.9 NC_000018.8	AC023440.4

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss1783346	HapMap-CEU	European	120	IG	1.000			1.000

	HapMap-HCB	Asian	90	IG	1.000			1.000

	HapMap-JPT	Asian	86	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.633	0.367	0.100	0.817	0.183

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.100+/-0.200	270	210	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .