Reference SNP(refSNP) Cluster Report: rs399251

Reference SNP(refSNP) Cluster Report: rs399251

refSNP ID: rs399251
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	80/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_020459.1:c.*4280G>C
NT_022184.14:g.50227266C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44208599 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs399251 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
ss519165	SC_JCM\|AC021225.4_36274	fwd/B	C/G	gccaataggaaggtaagattggggagaaag	tcagtaaatgtcacaaaagagactcctagt	07/12/00	04/07/04	80	Genomic	unknown
ss4322146	CGAP-GAI\|257458	fwd/B	C/G	gccaataggaaggtaagattggggagaaag	tcagtaaatgtcacaaaagagactcctagt	11/28/01	10/10/03	102	cDNA	unknown
ss4418891	LEE\|e507033	rev/T	C/G	actaggagtctcttttgtgacatttactga	ctttctccccaatcttaccttcctattggc	04/26/02	10/10/03	106	cDNA	unknown
ss9950434	BCM_SSAHASNP\|chr2.NT_022184.12_50227261	fwd/B	C/G	gccaataggaaggtaagattggggagaaag	tcagtaaatgtcacaaaagagactcctagt	06/27/03	10/10/03	116	Genomic	unknown
ss16243445	CGAP-GAI\|1484191	rev/T	C/G	actaggagtctcttttgtgacatttactga	ctttctccccaatcttaccttcctattggc	11/18/03	11/22/03	120	cDNA	unknown
ss23718171	PERLEGEN\|afd1271995	fwd/B	C/G	gccaataggaaggtaagattggggagaaag	tcagtaaatgtcacaaaagagactcctagt	08/10/04	09/13/04	123	Genomic	unknown
ss44208599	ABI\|hCV775693	fwd/	C/G	gccaataggaaggtaagattggggagaaag	tcagtaaatgtcacaaaagagactcctagt	07/18/05	11/03/06	126	Genomic	unknown
ss68379638	CSHL-HAPMAP\|perlegen:assay:24709.1271995:1	fwd/	C/G	gccaataggaaggtaagattggggagaaag	tcagtaaatgtcacaaaagagactcctagt	01/11/07	01/16/07	127	NA	unknown
ss80723170	HGSV\|Cor18507_SNV_20070510.chr2_71322984	fwd/	C/G	gccaataggaaggtaagattggggagaaag	tcagtaaatgtcacaaaagagactcctagt	11/26/07	11/26/07	130	Genomic	unknown

Fasta sequence (Legend)

 GGGTGTTTTA TGATATGTAA CATATGCCTC ATTAAAGTTG TTTTAAGAAA AGGATTCCCT
 GCCTCCCAAA CCATCCTTCA AGCATTAAAC ATTTTTGGAG GCTCATAATC AACAGGACAG
 AATAACTACT TAGTGATGAT TTACAGAGTG AAATATTTTA CTGTTTTGTA GTAAGCACAT
 TTTAGTAACT GTACACTAGT ACAATGTTTT TAAGATTTTA TCTCATTTTT GTCATATTAG
 CCTAAAATGT TTATTTTTAT TTAAAAAGTA GCCAATAGGA AGGTAAGATT GGGGAGAAAG
 S
 TCAGTAAATG TCACAAAAGA GACTCCTAGT AACACAATCT GAGGGAGCTT TTTCTTTTGA
 AATAAAGATG GTGCATCTGT CCCTTTACAG ATTTCTCTCC TGTCCCCTGG GACTGGGGAA
 GGTGAATCTC CTGCCTGACA CCTTGTAGAG ATTAGTGTAT CCAGCTATTC TATTGCCACG
 ATGCCTCTAA AAACCAGACT GACTGGGAAC AGCAGTAGGG GGTTGGCCAG TGAGGGCAGG
 TGACTAAGTG GTGTGCAGGA AACTCGCATG TTTCCCTGGG TTGGCTTCCT GCTCCCCTGT

GeneView

GeneView via analysis of contig annotation: PAIP2B poly(A) binding protein interacting protein 2B

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_022184->NM_020459

function

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


reference	NT_022184->NM_020459->	50227266	reverse	4839	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs399251 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838769.1	41244244	71148000	plus	C	alt_assembly_8	HuRef	HuRef	view	300
2	NW_927719.1	71193977	71262042	plus	C	alt_assembly_1	Celera	Celera	view	300
2	NT_022184.14	50227266	71264837	plus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
CGAP-C-25745	R16190 AC007881 H70499 Hs.102657

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank mRNA:
NM_020459.1	AB032981.1

UniGene Cluster ID
416735

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss23718171	AFD_EUR_PANEL	European	46	IG	0.609	0.348	0.043	1.000	0.783	0.217

	AFD_AFR_PANEL	African American	46	IG	0.391	0.391	0.217	0.371	0.587	0.413

	AFD_CHN_PANEL	Asian	48	IG	0.667	0.250	0.083	0.251	0.792	0.208

ss44208599	HapMap-CEU	European	120	IG	0.567	0.350	0.083	0.527	0.742	0.258

	HapMap-HCB	Asian	90	IG	0.489	0.422	0.089	1.000	0.700	0.300

	HapMap-JPT	Asian	88	IG	0.409	0.432	0.159	0.752	0.625	0.375

	HapMap-YRI	Sub-Saharan African	120	IG	0.367	0.533	0.100	0.254	0.633	0.367

ss519165	CEPH		184	AF					0.650	0.350

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.429+/-0.174	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: ILLUMINA, PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .