Reference SNP(refSNP) Cluster Report: rs16837598

Reference SNP(refSNP) Cluster Report: rs16837598

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/130
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
NG_008843.1:g.23151C>T
NM_153717.2:c.341C>T
NP_714928.1:p.Ala114Val
NT_006051.17:g.1818519C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48404349 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16837598 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
ss23363033	PERLEGEN\|afd3395033	fwd/B	C/T	cgccttccaacagcaatatcacagcattcg	cctgaaggccaaagtcatctaccccatcaa	08/10/04	09/13/04	123	Genomic	unknown
ss48404349	APPLERA_GI\|hCV25937312	rev/T	A/G	ttgatggggtagatgactttggccttcagg	cgaatgctgtgatattgctgttggaaggcg	09/28/05	11/03/06	126	Genomic	unknown
ss66515164	AFFY\|SNP_A-4219232	fwd/B	C/T	aatatcacagcattcg	cctgaaggccaaagtc	10/29/06	03/31/08	127	Genomic	unknown
ss68889090	PERLEGEN\|PGP03395033	fwd/B	C/T	cgccttccaacagcaatatcacagcattcg	cctgaaggccaaagtcatctaccccatcaa	01/30/07	03/31/08	127	Genomic	unknown
ss74907593	ILLUMINA\|ILMN_Human_1M_rs16837598	fwd/B	C/T	cgccttccaacagcaatatcacagcattcg	cctgaaggccaaagtcatctaccccatcaa	08/28/07	08/29/07	129	Genomic	unknown
ss76337810	AFFY\|AFFY_6_1M_SNP_A-4219232	fwd/B	C/T	aatatcacagcattcg	cctgaaggccaaagtc	08/28/07	08/30/07	129	Genomic	unknown
ss83059348	KRIBB_YJKIM\|KHS386063	fwd/B	C/T	cgccttccaacagcaatatcacagcattcg	cctgaaggccaaagtcatctaccccatcaa	11/30/07	12/04/07	130	Genomic	unknown
ss116852265	ILLUMINA-UK\|NA18507_000009087_NCBI36.1_chr4_5781975	fwd/B	C/T	cgccttccaacagcaatatcacagcattcg	cctgaaggccaaagtcatctaccccatcaa	01/18/09	01/18/09	130	Genomic	99 %

Fasta sequence (Legend)

 TCCATCCATC CACCTGTCTA TCCATCTGCC CACCCACCCA TTCATTCACC CATCCATCCA
 TCTATCCATC CATCTGTTTG TCCACCCATC CATCCATTTT CCTTCTGGCA AGGAAGAGCT
 AATATGAATC TAAATGTGCC TATCATGGTC CCTTTCTGAG GCTGCTATTA CAAATGGGAT
 GTGGCATTTT GGAAAAACTT GACAACTTAT CCTTCATTTT ACAGAAAGTT TCCCATGCCG
 TTTGTGTCTT TCCCTCCCAG GAATGTGAGC CGCCTTCCAA CAGCAATATC ACAGCATTCG
 Y
 CCTGAAGGCC AAAGTCATCT ACCCCATCAA TCAGAAGTTC CGGGTGAGAG TCCTGAGCTC
 CATCATAGAA AGCCAGTTAC TTCCGTCATG TGCCAGAGAT TGGGAGGAAA GTGGGGGGAT
 TAACTGTGTG ATGTTTGGTC CTGTTTGAGG GTTTTATGGC AAGTCATTTT AGTAGGGATA
 GTTTTGAGGC TCAGGAACAG GACATGCCCA TGGTAACCAC GGTACGGAAG TTCCATGGTT
 CCTTGTATCC CCAGGGACAC GAGGTAACAG CACAGTAGGA CAGCTCCCTC TCTGCCTTTT

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
NC_000004.9

dbSNP Blast Analysis

UniGene Cluster ID
552571

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss23363033	AFD_EUR_PANEL	European	42	IG	1.000				1.000

	AFD_AFR_PANEL	African American	36	IG	0.778	0.167	0.056	0.200	0.861	0.139

	AFD_CHN_PANEL	Asian	42	IG	1.000				1.000

ss48404349	HapMap-CEU	European	118	IG	0.983	0.017		1.000	0.992	0.008

	HapMap-HCB	Asian	90	IG	1.000				1.000

	HapMap-JPT	Asian	90	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	118	IG	0.661	0.305	0.034	1.000	0.814	0.186

	AGI_ASP population	multiple	78	IG	0.846	0.077	0.077	0.001	0.885	0.115

ss66515164	HapMap-CEU	European	118	GF	0.983	0.017			0.992	0.008

	HapMap-HCB	Asian	90	GF	1.000				1.000

	HapMap-JPT	Asian	90	GF	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.650	0.317	0.033		0.808	0.192

ss68889090	HapMap-CEU	European	120	GF	0.983	0.017			0.992	0.008

	HapMap-HCB	Asian	90	GF	1.000				1.000

	HapMap-JPT	Asian	90	GF	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.650	0.317	0.033		0.808	0.192

ss76337810	ICMHP		8	IG	1.000				1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.110+/-0.207	1221	1006	276	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .