Reference SNP(refSNP) Cluster Report: rs2442627

Reference SNP(refSNP) Cluster Report: rs2442627

refSNP ID: rs2442627
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001147.1:c.931-1757T>A
NM_024596.2:c.2214+16606A>T
NT_023736.16:g.6361464A>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3423963 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2442627 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
ss3423963	SC_JCM\|AC018398.6_92289	fwd/B	A/T	aataagaggcagtattattcatgaactgat	taaacttggaactgtgttgagggacttttg	09/24/01	04/07/04	100	Genomic	unknown
ss23335578	PERLEGEN\|afd1857256	rev/T	A/T	caaaagtccctcaacacagttccaagttta	atcagttcatgaataatactgcctcttatt	08/10/04	09/13/04	123	Genomic	unknown
ss66029379	AFFY\|SNP_A-1655126	rev/T	A/T	gtccctcaacacagttccaagttta	atcagttcatgaataatactgcctc	10/26/06	10/26/06	127	Genomic	unknown

Fasta sequence (Legend)

 GTCAATGCTT TCAACCCAAG AGCATACCAT TTAGGATACA GAATTAACTT CAATATATGT
 ACATGAATCC TCAAACCAAA GTAGCTTATT CAGCTGGTTT ATGAAATAGA TTTTTAAAAA
 GAAATATTGA TAGAAGTGAG CAGCACTGAC CATTTTGTTG ACTGCAGGCA AATAAGAGGC
 AGTATTATTC ATGAACTGAT
 W
 TAAACTTGGA ACTGTGTTGA GGGACTTTTG GCCTATTTAC CAAAGGGTCA GGTTTCTCTG
 TTTTTGGCAG CATGATGTCA GTGGAAAAAA AACATAACAG GAATCAAAGA GACCTTATTC
 AAATCCTATA TATCACTTAG AAGGTGAGTA ACTGATCAAA ATCGAACTTT GCTAAATCTT
 TTCTCCTTTC AAAAATGCAG

GeneView

GeneView via analysis of contig annotation: MCPH1 microcephalin 1

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: ANGPT2 angiopoietin 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_023736->NM_024596

function

HuRef

NW_001839109->NM_024596

function

Celera

NW_923840->NM_024596

function

reference

NT_023736->NM_001147

function

HuRef

NW_001839109->NM_001147

function

Celera

NW_923840->NM_001147

function

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


reference	NT_023736->NM_024596->NP_078872	6361464	forward	intron

HuRef	NW_001839109->NM_024596->NP_078872	682686	reverse	intron

Celera	NW_923840->NM_024596->NP_078872	4170447	forward	intron

reference	NT_023736->NM_001147->NP_001138	6361464	reverse	intron

HuRef	NW_001839109->NM_001147->NP_001138	682686	forward	intron

Celera	NW_923840->NM_001147->NP_001138	4170447	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2442627 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	682686	6156024	plus	T	alt_assembly_8	HuRef	HuRef	view	200
8	NW_923840.1	4170447	6351544	minus	A	alt_assembly_1	Celera	Celera	view	200
8	NT_023736.16	6361464	6361464	minus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000008.6 AX087869

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC011835.8 AC018398.10 NC_000008.9	AC091095.2 AF257499.3

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/T	T/T	HWP	A	T
ss23335578	AFD_EUR_PANEL	European	48	IG	0.083	0.917	1.000	0.042	0.958

	AFD_AFR_PANEL	African American	46	IG	0.174	0.826	0.655	0.087	0.913

	AFD_CHN_PANEL	Asian	48	IG		1.000			1.000

ss3423963	AfAm	African American	12	IG		1.000			1.000

	Caucasian	European	22	IG	0.091	0.909	1.000	0.045	0.955

	Asian	Asian	12	IG		1.000			1.000

	CEPH	European	12	IG	0.167	0.833	1.000	0.083	0.917

	PDpanel	Global	48	IG	0.125	0.875	0.752	0.062	0.938

	HapMap-CEU	European	120	IG	0.150	0.850	0.584	0.075	0.925

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	88	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.133	0.867	0.752	0.067	0.933

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.081+/-0.184	379	306	15	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .