Reference SNP(refSNP) Cluster Report: rs927628

Reference SNP(refSNP) Cluster Report: rs927628

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/130
Map to Genome Build:	36.3

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

HGVS Names
NT_007592.14:g.5868481C>T
XM_001128918.2:c.114-12524A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44732536 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs927628 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
ss1365519	TSC-CSHL\|TSC0244208	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	09/06/00	04/07/04	86	Genomic	95 %
ss1928260	KWOK\|OVLP-000925-679402	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	10/06/00	10/10/03	87	Genomic	99 %
ss12843325	SC_SNP\|NT_007592.13_5868481	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	10/21/03	11/17/03	119	Genomic	unknown
ss22498085	SSAHASNP\|WGSA-200403-chr6.chr6.NT_007592.13_5868481	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	03/21/04	03/21/04	121	Genomic	unknown
ss23939118	PERLEGEN\|afd0370419	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	08/10/04	09/13/04	123	Genomic	unknown
ss44732536	ABI\|hCV3118551	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	07/19/05	11/03/06	126	Genomic	unknown
ss77824952	HGSV\|Cor12156_SNV_20070510.chr6_15118209	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	10/09/07	10/14/07	129	Genomic	unknown
ss93400627	BCMHGSC_JDW\|JWB-2101224	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	02/26/08	03/04/08	129	Genomic	unknown
ss98475499	HUMANGENOME_JCVI\|1103652790162	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	04/01/08	04/01/08	130	Genomic	unknown
ss109777299	1000GENOMES\|CEU.trio.12.15.2008_1455401_chr6_15118209	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	12/15/08	12/16/08	130	Genomic	unknown
ss113940604	1000GENOMES\|NA19240_2008_12_16_1309608_chr6_15118209	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	12/18/08	12/18/08	130	Genomic	unknown
ss116320674	ILLUMINA-UK\|NA18507_000022698_NCBI36.1_chr6_15118209	fwd/B	C/T	aaaaaaaataaaattgcttttgaatactga	gtgcccaaagttaaaaaactataaatgggt	01/17/09	01/17/09	130	Genomic	99 %

Fasta sequence (Legend)

 ACACACAGCT TCCTCCCCCA TGAACACCAC ACAAACCAAA CAGAAACCCA GGGACAGTAC
 AGAACAATTA GGGTTAGAAA GGAAACAAAT AAAATCACTT TTTTCTCCTC ACACATCTTA
 ATCTCAGAGC CACTACAAAA TTAGACTCAG CAAATTCCAC TTGAAATTTT AATATGACTA
 TAAAACTATT TGGCAATGTG ATAATTGGCA TAAATTAGAA CTTCATAGTT AAACAGAACA
 GTTGAACAGT TCAGGTTAAA ATTGCTTTTG AAAAAAAATA AAATTGCTTT TGAATACTGA
 Y
 GTGCCCAAAG TTAAAAAACT ATAAATGGGT CCTTGGTCAG CTAATTCCAA AACAATACAC
 CCCAGACTTC TGTTAACACT TAATTAACAC AAAACTAAAA CAACATGCAG AACAATGTTG
 GAATCTGGTG TCCAGAAAAG AATTCAGCCA ATTTATGGTT GTCAACCACT TAATGCAACT
 TGAGCCTGGG ACAAAACAGA ATTCTAAACC TTCTCCCATT TCCAATTATG TAAACTGCAA
 AATCAGCTGC TGCCACAAGT ATGCATAAAT GTAATCCCCA ATTTTCCAAG TTAAACCTAG

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_007592 ABBA01022152 AL138720.12 AL138720.5

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss1365519	TSC_42_AA		82	AF					0.659		0.341

	TSC_42_C		80	AF					0.613		0.387

	TSC_42_A		82	AF					0.460		0.540

	CHMJ	Asian	74	IG					0.527	0.027	0.446

ss23939118	AFD_EUR_PANEL	European	48	IG	0.375	0.417	0.208	0.527	0.583		0.417

	AFD_AFR_PANEL	African American	46	IG	0.304	0.609	0.087	0.200	0.609		0.391

	AFD_CHN_PANEL	Asian	48	IG	0.125	0.667	0.208	0.100	0.458		0.542

ss44732536	HapMap-CEU	European	120	IG	0.317	0.500	0.183	1.000	0.567		0.433

	HapMap-HCB	Asian	90	IG	0.156	0.511	0.333	0.752	0.411		0.589

	HapMap-JPT	Asian	90	IG	0.311	0.489	0.200		0.556		0.444

	HapMap-YRI	Sub-Saharan African	120	IG	0.417	0.450	0.133	1.000	0.642		0.358

	AoD_African_American		90	AF					0.670		0.330

	AoD_Caucasian		92	AF					0.490		0.510

	AoD_Chinese		90	AF					0.390		0.610

	AoD_Japanese		90	AF					0.470		0.530

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict	Additional Freq. Data
	0.495+/-0.051	582	459	15	0	ALFRED: The Allele Frequency Database

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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .