Reference SNP(refSNP) Cluster Report: rs884694

Reference SNP(refSNP) Cluster Report: rs884694

refSNP ID: rs884694
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_145000.2:c.91+8C>A
NT_006576.15:g.36274177G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1312088 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs884694 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
ss1312088	TSC-CSHL\|TSC0027071	fwd/B	G/T	gtcacagaatatgcaactcatgagctggac	gactcaccttgctgtcgccggtcctcctgc	09/06/00	10/25/06	86	Genomic	95 %
ss17865881	CSHL-HAPMAP\|CSHL-HuCC-200402.chr5.NT_006576.14_18753526	fwd/B	G/T	gtcacagaatatgcaactcatgagctggac	gactcaccttgctgtcgccggtcctcctgc	02/19/04	03/04/04	120	Genomic	unknown
ss22341012	SSAHASNP\|WGSA-200403-chr5.chr5.NT_006576.14_18753526	fwd/B	G/T	gtcacagaatatgcaactcatgagctggac	gactcaccttgctgtcgccggtcctcctgc	03/21/04	03/21/04	121	Genomic	unknown
ss23990090	PERLEGEN\|afd2508494	fwd/B	G/T	gtcacagaatatgcaactcatgagctggac	gactcaccttgctgtcgccggtcctcctgc	08/10/04	09/13/04	123	Genomic	unknown
ss44644674	ABI\|hCV8811257	fwd/B	G/T	gtcacagaatatgcaactcatgagctggac	gactcaccttgctgtcgccggtcctcctgc	07/19/05	07/19/05	126	Genomic	unknown
ss68932450	PERLEGEN\|PGP02508494	fwd/B	G/T	gtcacagaatatgcaactcatgagctggac	gactcaccttgctgtcgccggtcctcctgc	01/30/07	08/14/07	127	Genomic	unknown
ss75115247	ILLUMINA\|ILMN_Human_1M_rs884694	fwd/B	G/T	gtcacagaatatgcaactcatgagctggac	gactcaccttgctgtcgccggtcctcctgc	08/28/07	08/29/07	129	Genomic	unknown
ss86185588	HGSV\|Cor18517_SNV_20070510.chr5_36337177	fwd/B	G/T	gtcacagaatatgcaactcatgagctggac	gactcaccttgctgtcgccggtcctcctgc	12/06/07	12/11/07	130	Genomic	unknown
ss93062027	BCMHGSC_JDW\|JWB-1963990	fwd/B	G/T	gtcacagaatatgcaactcatgagctggac	gactcaccttgctgtcgccggtcctcctgc	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 CTGAAATCCC CCTTGTAGCT GACTCAGCCT TGCTCAGATG GGTGTTTTGA ATTAGACAAA
 ATCTAGCATA CTCTAAAAAA CACAGTGGCT AGAAGTTTAA GCATGTAAGT TTCAGAATGA
 CAGCTCCAAG GAATATGCAT TCTTGACAGT CTTCCATAGT CCTCTAAAAA TCAATAGTGA
 ATCCAAGTTA ACCCACCCTT ATGCATCACT ATTATGTCAG AGCTTCCCCG GGTCCTTCAC
 CAGCCCACCA TTCTTCCTGG AATGCAAATG CACAGAAGGT CACAGAATAT GCAACTCATG
 AGCTGGAC
 K
 GACTCACCTT GCTGTCGCCG GTCCTCCTGC AGCTTCAGTT TACAGGTGTG CAAACTGCCA
 GGCAGGTGGC TGCTGCCTTT TCTTGGTATG GTAGTCATGG TCCTAGCAGT ATGGCTGTGA
 CTCAAGGATC ACTAGGGCAC CTCCTTCTCT GGCCAGTCAC CTAAAGTGGC CTTCACCAGA
 CACCCAGAAA TACATAGATT CATGCAGATC TTGTCTTTGC ATGTACAACA TATACTCCTC
 TACTAAACTT CCAAGCTTTT TCCAGTCATG ATTCTTGAAA TAAATAATCA CCAATGTTAC
 TTCTCCTAAA TATAAAGATG CCCATTCATT TGGTTAAAAA CACAACTTAA TTCCTTCATT
 TCAAAACAAA TTGAAACTAA ACCTCCTTAT AGAGTAAAAT TCTACAAATT AACTATTTCT
 A

GeneView

GeneView via analysis of contig annotation: RANBP3L RAN binding protein 3-like

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_006576->NM_145000

function

HuRef

NW_001838933->NM_145000

function

Celera

NW_922596->NM_145000

function

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


reference	NT_006576->NM_145000->NP_659437	36274177	reverse	intron

HuRef	NW_001838933->NM_145000->NP_659437	595671	reverse	intron

Celera	NW_922596->NM_145000->NP_659437	1897605	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs884694 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_922596.1	1897605	36187091	plus	T	alt_assembly_1	Celera	Celera	view	308
5	NW_001838933.1	595671	36253060	plus	T	alt_assembly_8	HuRef	HuRef	view	308
5	NT_006576.15	36274177	36337177	plus	G	ref_assembly	reference	reference	view	308

NCBI Resource Links

Submitter-Referenced
GenBank
NT_006576

dbSNP Blast Analysis
GenBank HTGS Finished:
AC026439.4 AC114277.2 NC_000005.8

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss1312088	HapMap-CEU	European	118	IG	0.102	0.356	0.542	0.371	0.280	0.720

	HapMap-HCB	Asian	88	IG	0.250	0.568	0.182	0.371	0.534	0.466

	HapMap-JPT	Asian	90	IG	0.533	0.400	0.067		0.733	0.267

	HapMap-YRI	Sub-Saharan African	120	IG	0.417	0.483	0.100	0.584	0.658	0.342

	CHMJ	Asian	74	IG					0.595	0.405

ss23990090	AFD_EUR_PANEL	European	48	IG		0.292	0.708	0.439	0.146	0.854

	AFD_AFR_PANEL	African American	46	IG	0.130	0.565	0.304	0.439	0.413	0.587

	AFD_CHN_PANEL	Asian	48	IG	0.333	0.458	0.208	0.752	0.562	0.438

ss68932450	HapMap-CEU	European	120	GF	0.100	0.333	0.567		0.267	0.733

	HapMap-HCB	Asian	90	GF	0.244	0.556	0.200		0.522	0.478

	HapMap-JPT	Asian	90	GF	0.533	0.400	0.067		0.733	0.267

	HapMap-YRI	Sub-Saharan African	120	GF	0.417	0.483	0.100		0.658	0.342

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss1312088	269	77	120	70
ss23990090	71	11	31	29
ss68932450	269	77	120	72

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs884694	332	88	149	94

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
577	ss1312088	G/T	CSHL-HAPMAP	HapMap-CEU	NA12813	CEPH1454.13	r23_ch5_CEU_perlegen:genotyping_1.0.0	2870359
577	ss68932450	T/T	CSHL-HAPMAP	HapMap-CEU	NA12813	CEPH1454.13	chr5-HapMap-CEU

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

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 .