Reference SNP(refSNP) Cluster Report: rs702808

Reference SNP(refSNP) Cluster Report: rs702808

refSNP ID: rs702808
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:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_001568.2:c.206-250A>G
NT_008046.15:g.22470727T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44855906 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs702808 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
ss1191880	KWOK\|OVLP-000804-634836	fwd/T	A/G	tttcacatccctctgtcaccccaaggctgt	tattctctagtttccctcaagagtaggaag	09/02/00	10/10/03	86	Genomic	99 %
ss1265817	KWOK\|OVLP-000804-633243	fwd/T	A/G	tttcacatccctctgtcaccccaaggctgt	tattctctagtttccctcaagagtaggaag	09/02/00	10/10/03	86	Genomic	96 %
ss2020472	KWOK\|OVLP-000925-583891	fwd/T	A/G	tttcacatccctctgtcaccccaaggctgt	tattctctagtttccctcaagagtaggaag	10/06/00	10/25/06	87	Genomic	99 %
ss2063909	KWOK\|OVLP-000925-576667	fwd/T	A/G	tttcacatccctctgtcaccccaaggctgt	tattctctagtttccctcaagagtaggaag	10/07/00	10/10/03	87	Genomic	96 %
ss3669425	SC_JCM\|AC020991.3_84898	fwd/T	A/G	tttcacatccctctgtcaccccaaggctgt	tattctctagtttccctcaagagtaggaag	09/24/01	10/10/03	100	Genomic	unknown
ss6527202	WI_SSAHASNP\|NT_008046.11_18228777	rev/B	C/T	cttcctactcttgagggaaactagagaata	acagccttggggtgacagagggatgtgaaa	02/12/03	10/10/03	111	Genomic	unknown
ss22705437	SSAHASNP\|WGSA-200403-chr8.chr8.NT_008046.14_22470727	rev/B	C/T	cttcctactcttgagggaaactagagaata	acagccttggggtgacagagggatgtgaaa	03/21/04	03/21/04	121	Genomic	unknown
ss24538893	PERLEGEN\|afd1969725	rev/B	C/T	cttcctactcttgagggaaactagagaata	acagccttggggtgacagagggatgtgaaa	08/10/04	09/13/04	123	Genomic	unknown
ss44855906	ABI\|hCV8848746	rev/B	C/T	cttcctactcttgagggaaactagagaata	acagccttggggtgacagagggatgtgaaa	07/19/05	11/03/06	126	Genomic	unknown
ss78618228	HGSV\|Cor12878_SNV_20070510.chr8_109321730	rev/B	C/T	cttcctactcttgagggaaactagagaata	acagccttggggtgacagagggatgtgaaa	10/17/07	10/20/07	129	Genomic	unknown
ss80863686	HGSV\|Cor18507_SNV_20070510.chr8_109321730	rev/B	C/T	cttcctactcttgagggaaactagagaata	acagccttggggtgacagagggatgtgaaa	11/26/07	11/27/07	130	Genomic	unknown
ss93946055	BCMHGSC_JDW\|JWB-2508496	rev/B	C/T	cttcctactcttgagggaaactagagaata	acagccttggggtgacagagggatgtgaaa	02/26/08	03/05/08	129	Genomic	unknown

Fasta sequence (Legend)

 TAGTATAGTA AAAGGAACGA TAGAATTTGG TTTGAGAGAT TATAGAGCTG GATTTGTGGT
 TAAAAGAGAT TATTTAATGG ATTTAAATTC CATTCAACCT AGTTGATAGC CTGTAATAGT
 AATATGTAAA TCCCTCTGAG TTTTTCTTCA AAAACTCTGG GATAATATTC ACCTAAGAAA
 ATTAAATGAG AACAAATATA AAAACACTTG GAAAGAAGTT TCTGCAATGG AGAATTAAAT
 GATAGATAAT TGGGTCCTAC CCTTTTTTTC TTTCACATCC CTCTGTCACC CCAAGGCTGT
 R
 TATTCTCTAG TTTCCCTCAA GAGTAGGAAG AGGATTCCCT TTTCCTTTTT GTGCCTTTGT
 ATTAGTAGAA AAAAGAAATT AGGGATCGGG GACATTTCTG ACTGAGTAGC CCATGGCATA
 TGAATATATT GGGGGTAAAT AAATATATGT ATAGTTTAAA TACACTGAAA AATTTCCAGA
 CATTCTCATG ATGAGTAGCA CAATTTAACA TTCCTTAACA TTGTAGTGCT CTTCTGCATT
 TTTAATTAGC TTTGAGAGAG AAAAGAACCA CAGTGGTTGC ACAACTGAAA CAGCTTCAGG

GeneView

GeneView via analysis of contig annotation: EIF3E eukaryotic translation initiation factor 3, subunit E

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_008046->NM_001568

function

HuRef

NW_001839136->NM_001568

function

Celera

NW_923984->NM_001568

function

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


reference	NT_008046->NM_001568->NP_001559	22470727	reverse	intron

HuRef	NW_001839136->NM_001568->NP_001559	22515531	reverse	intron

Celera	NW_923984->NM_001568->NP_001559	22405017	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs702808 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_001839136.1	22515531	104574007	minus	C	alt_assembly_8	HuRef	HuRef	view	300
8	NW_923984.1	22405017	105439699	minus	T	alt_assembly_1	Celera	Celera	view	300
8	NT_008046.15	22470727	109321730	minus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008046 AC018588 AC020991.3 AP001331 AP001331.1

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC087620.6 NC_000008.9	AC018588.5 AC020991.4 AC083931.4 AC084258.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24538893	AFD_EUR_PANEL	European	46	IG	0.261	0.435	0.304	0.584	0.478	0.522

	AFD_AFR_PANEL	African American	42	IG	0.238	0.619	0.143	0.254	0.548	0.452

	AFD_CHN_PANEL	Asian	48	IG	0.208	0.500	0.292	1.000	0.458	0.542

ss44855906	HapMap-CEU	European	120	IG	0.217	0.550	0.233	0.439	0.492	0.508

	HapMap-HCB	Asian	90	IG	0.222	0.489	0.289	1.000	0.467	0.533

	HapMap-JPT	Asian	88	IG	0.432	0.477	0.091	0.655	0.670	0.330

	HapMap-YRI	Sub-Saharan African	120	IG	0.200	0.417	0.383	0.294	0.408	0.592

	AoD_African_American		90	AF					0.480	0.520

	AoD_Caucasian		92	AF					0.510	0.490

	AoD_Chinese		90	AF					0.540	0.460

	AoD_Japanese		90	AF					0.550	0.450

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.500+/-0.002	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: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .