Reference SNP(refSNP) Cluster Report: rs696221

Reference SNP(refSNP) Cluster Report: rs696221

refSNP ID: rs696221
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:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_183352.1:c.*69G>A
NT_022517.17:g.10282876C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss91996109 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs696221 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
ss896230	KWOK\|OVLP-000804-128310	rev/T	A/G	aggactgccccttcctgggccaactaacca	acaactgggaagagcccccaactccaacag	09/01/00	10/10/03	86	Genomic	99 %
ss1009747	KWOK\|OVLP-000804-177710	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	09/02/00	10/10/03	86	Genomic	97 %
ss1062349	KWOK\|OVLP-000804-138088	rev/T	A/G	aggactgccccttcctgggccaactaacca	acaactgggaagagcccccaactccaacag	09/02/00	10/10/03	86	Genomic	89 %
ss1529949	LEE\|523893	rev/T	A/G	aggactgccccttcctgggccaactaacca	acaactgggaagagcccccaactccaacag	09/13/00	10/10/03	86	cDNA	unknown
ss1599922	KWOK\|OVLP-000925-350041	rev/T	A/G	aggactgccccttcctgggccaactaacca	acaactgggaagagcccccaactccaacag	10/04/00	05/16/04	87	Genomic	99 %
ss1638242	KWOK\|OVLP-000925-338390	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	10/04/00	10/10/03	87	Genomic	97 %
ss1658281	KWOK\|OVLP-000925-346649	rev/T	A/G	aggactgccccttcctgggccaactaacca	acaactgggaagagcccccaactccaacag	10/05/00	10/10/03	87	Genomic	89 %
ss2425853	HGBASE\|SNP000013602	rev/T	A/G	tgccccttcctgggccaactaacca	acaactgggaagagcccccaactcc	11/07/00	10/10/03	89	cDNA	unknown
ss2512389	SC_JCM\|AC023501.13_55397	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	11/03/00	10/10/03	92	Genomic	unknown
ss4419475	LEE\|e523893	rev/T	A/G	aggactgccccttcctgggccaactaacca	acaactgggaagagcccccaactccaacag	04/26/02	10/10/03	106	cDNA	unknown
ss4438150	LEE\|e1580352	rev/T	A/G	aggactgccccttcctgggccaactaacca	acaactgggaagagcccccaactccaacag	04/26/02	10/10/03	106	cDNA	unknown
ss6451561	WI_SSAHASNP\|NT_005927.13_10272142	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	02/12/03	10/10/03	111	Genomic	unknown
ss11537257	WI_SSAHASNP\|chr3.NT_005927.15_10271722	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	07/03/03	10/10/03	116	Genomic	unknown
ss16229091	CGAP-GAI\|1466254	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	11/18/03	11/22/03	120	cDNA	unknown
ss24608166	PERLEGEN\|afd0793587	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	08/10/04	09/13/04	124	Genomic	unknown
ss66624407	ILLUMINA\|HumanHap300v1.1_rs696221	fwd/T	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	11/09/06	11/09/06	127	Genomic	unknown
ss67522077	ILLUMINA\|HumanHap550v1.1_rs696221	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	11/14/06	11/14/06	127	Genomic	unknown
ss67888907	ILLUMINA\|HumanHap650Yv1.0_rs696221	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	11/14/06	11/14/06	127	Genomic	unknown
ss70898501	ILLUMINA\|HumanHap550v3.0__rs696221	rev/T	A/G	aggactgccccttcctgggccaactaacca	acaactgggaagagcccccaactccaacag	04/20/07	03/31/08	130	Genomic	unknown
ss71493307	ILLUMINA\|HumanHap650Yv3.0_rs696221	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	04/23/07	04/23/07	127	Genomic	unknown
ss75469783	ILLUMINA\|ILMN_Human_1M_rs696221	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	08/28/07	08/29/07	129	Genomic	unknown
ss78566552	HGSV\|Cor18507_SNV_20070510.chr3_10317876	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	10/19/07	10/20/07	129	Genomic	unknown
ss79240211	ILLUMINA\|HumanHap300v2.0_rs696221	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	04/18/07	11/18/07	130	Genomic	unknown
ss81812147	HGSV\|Cor18956_SNV_20070510.chr3_10317876	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	11/30/07	12/01/07	130	Genomic	unknown
ss83520090	KRIBB_YJKIM\|KHS480850	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	12/04/07	12/05/07	130	Genomic	unknown
ss84318347	HGSV\|Cor19129_SNV_20070510.chr3_10317876	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	12/06/07	12/07/07	130	Genomic	unknown
ss84369797	HGSV\|Cor18517_SNV_20070510.chr3_10317876	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	12/06/07	12/07/07	130	Genomic	unknown
ss91996109	BCMHGSC_JDW\|JWB-1556816	fwd/B	C/T	ctgttggagttgggggctcttcccagttgt	tggttagttggcccaggaaggggcagtcct	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATGACTTTAT TTAGTTCCTT TGGAAACAAA ACCCCCCAAA TAATGCCTGA ACCCAAAGGT
 ACATAAAAAT GACCCAAAAT AGATTTGAAC ATCACTTGTA GTTTCTTCCT CGTAACATGA
 GTGCTTTCAG CTGGACAGTA GATTACAAAG CATCTCCGAT CACGTTAAGG CAGATGATCA
 ATCTGTGGCT GCATCTGTAA CTCCTCCTGG GAAAATAATC CTGTTGGAGT TGGGGGCTCT
 TCCCAGTTGT
 Y
 TGGTTAGTTG GCCCAGGAAG GGGCAGTCCT GGAGCTGGCG GGTGGGGAGC CAGGCCCCAC
 CTGTCTTGTC ACTGCTCGTT CTGCTGGCCC TCTGTCACTG ATGCTGATAC GGAGCCCTGG
 CCCTTGTTGA CATCACTGAT GCACACCCAC TGCCCATCAA CTGACTCCTT CCACAGGGTC
 ACCTGCGAGT CAGTGCACAA GCAGATTATC ACGGGTCTGT GCCCTTCCCT CTGCTGTCCC
 CTAAATATGA

GeneView

GeneView via analysis of contig annotation: SEC13 SEC13 homolog (S. cerevisiae)

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_022517->NM_183352

function

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


reference	NT_022517->NM_183352->	10282876	reverse	1157	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs696221 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_001838876.2	64198	10278236	minus	G	alt_assembly_8	HuRef	HuRef	view	200
3	NW_921651.1	10278684	10278684	plus	C	alt_assembly_1	Celera	Celera	view	200
3	NT_022517.17	10282876	10317876	plus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_005927 AC008116 AC012515 AC023501.12 AC023501.13 BE621944 Hs.227949

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank STS:	GenBank mRNA:
NM_183352.1	BV178359.1	AB209554.1 BC002634.2 BC006167.1 BC091506.1

UniGene Cluster ID
166924

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	A	C	G	T
ss1599922	CEPH		184	AF						0.390		0.610

	HapMap-CEU	European	120	IG	0.150	0.433	0.417	0.527		0.367		0.633

	HapMap-HCB	Asian	90	IG		0.022	0.978			0.011		0.989

	HapMap-JPT	Asian	90	IG		0.044	0.956			0.022		0.978

	HapMap-YRI	Sub-Saharan African	120	IG	0.067	0.250	0.683	0.439		0.192		0.808

	CHMJ	Asian	74	IG					0.973		0.027

ss24608166	AFD_EUR_PANEL	European	48	IG	0.250	0.458	0.292	0.752		0.479		0.521

	AFD_AFR_PANEL	African American	46	IG		0.435	0.565	0.200		0.217		0.783

	AFD_CHN_PANEL	Asian	48	IG			1.000					1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.299+/-0.245	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .