Reference SNP(refSNP) Cluster Report: rs11577368

Reference SNP(refSNP) Cluster Report: rs11577368

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/130
Map to Genome Build:	36.3

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

HGVS Names
NM_152268.2:c.84G>T
NP_689481.2:p.Arg28Ser
NT_032977.8:g.25196670C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44049164 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11577368 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
ss16390777	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_032977.6_16787822	fwd/T	A/C	ccgccctcttcttggggcacagtggtgaaa	ctgcaaggaacatacccagagagctggcgg	02/17/04	03/04/04	120	Genomic	unknown
ss44049164	ABI\|hCV3155030	fwd/T	A/C	ccgccctcttcttggggcacagtggtgaaa	ctgcaaggaacatacccagagagctggcgg	07/18/05	03/31/08	126	Genomic	unknown
ss48408051	APPLERA_GI\|hCV3155030	rev/B	G/T	ccgccagctctctgggtatgttccttgcag	tttcaccactgtgccccaagaagagggcgg	09/28/05	11/03/06	126	Genomic	unknown
ss68766273	PERLEGEN\|PGP00699472	fwd/T	A/C	ccgccctcttcttggggcacagtggtgaaa	ctgcaaggaacatacccagagagctggcgg	01/30/07	03/31/08	127	Genomic	unknown
ss74817019	AFFY\|SNP_M-313892	fwd/T	A/C	ccgccctcttcttggggcacagtggtgaaa	ctgcaaggaacatacccagagagctggcgg	08/09/07	08/09/07	128	Genomic	unknown
ss74893246	ILLUMINA\|ILMN_Human_1M_rs11577368	fwd/T	A/C	ccgccctcttcttggggcacagtggtgaaa	ctgcaaggaacatacccagagagctggcgg	08/28/07	08/29/07	129	Genomic	unknown
ss99208321	HUMANGENOME_JCVI\|1103675096564	fwd/T	A/C	ccgccctcttcttggggcacagtggtgaaa	ctgcaaggaacatacccagagagctggcgg	04/03/08	04/03/08	130	Genomic	unknown
ss108201903	1000GENOMES\|CEU.trio.12.15.2008_65241_chr1_54997339	fwd/T	A/C	ccgccctcttcttggggcacagtggtgaaa	ctgcaaggaacatacccagagagctggcgg	12/15/08	12/15/08	130	Genomic	unknown

Fasta sequence (Legend)

 CCAGAGCTCT GCCGGGCTGA GGCTGGGCAT GTTGACTTTC TGGCCCCCGA TGGCCTGCAT
 CTCCTGGTCT ATCACTCGCA CGAGCTTCTC CATGGCACGG ACGGTATATG GCAGGAGGTG
 GTAACAGCCG GGGCTTGCTG GGTAGATCAG GCCCACCTGC AGCATCAGCC GCTGGCTCTT
 ACAGGTCAGG TCATCAGATT TGTCCTGCAG GGAGAGCACC CGGTCTTCCC GAAGGTTCTG
 TGGCTGGAAC ACACGAGACA GCAGCAGGCG CCGCCCTCTT CTTGGGGCAC AGTGGTGAAA
 M
 CTGCAAGGAA CATACCCAGA GAGCTGGCGG CTGCAGGTGG CCAGGGCGGG CAATGCTCTG
 CATCTTGTCA GCAGCCCTTC CATGACACCC TGGCACCGGG AAGCACAGGC ACCTGAGGAA
 AAATGAGTTG TGTGAGAATG AGCCTCATCC GTGTTCCAAC ACCATGAAGC AGCCAACCCA
 GCCTGCTCTC AACAAACTTC GAAGGCAGCC ACTGATTTTG CAGATACAAA TCCTTCCATT
 TCTAATATCC TAGCAGATCA AAGCACTATT TCTCTAACCT CTTACTTCCG TTTTTGAAAA

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_032977 ABBA01074707

dbSNP Blast Analysis

UniGene Cluster ID
380169

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss44049164	HapMap-CEU	European	116	IG	0.052	0.276	0.672		0.190	0.810

	HapMap-HCB	Asian	88	IG	0.045	0.136	0.818		0.114	0.886

	HapMap-JPT	Asian	86	IG	0.023	0.186	0.791		0.116	0.884

	HapMap-YRI	Sub-Saharan African	116	IG		0.155	0.845		0.078	0.922

ss48408051	AGI_ASP population	multiple	74	IG	0.027	0.054	0.919	0.005	0.054	0.946

ss68766273	HapMap-CEU	European	120	GF	0.067	0.283	0.650		0.208	0.792

	HapMap-HCB	Asian	90	GF	0.044	0.133	0.822		0.111	0.889

	HapMap-JPT	Asian	90	GF	0.022	0.222	0.756		0.133	0.867

	HapMap-YRI	Sub-Saharan African	120	GF		0.150	0.850		0.075	0.925

Concordant Genotype	Total Sample	A/A	A/C	C/C
ss44049164	1205	15	258	904
ss48408051	39
ss68766273	268	7	53	208
ss99208321	1		1

RefSNP Genotype Summary	Total Individual	A/A	A/C	C/C
rs11577368	1247	15	266	925

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
538	ss44049164	C/C	CSHL-HAPMAP	HapMap-CEU	NA12753	CEPH1447.02	r27_ch1_CEU_illumina:human_1m_beadchip
538	ss68766273	C/C	CSHL-HAPMAP	HapMap-CEU	NA12753	CEPH1447.02	chr1-HapMap-CEU
636	ss44049164	C/C	CSHL-HAPMAP	HapMap-CEU	NA12891	CEPH1463.15	r27_ch1_CEU_illumina:human_1m_beadchip
636	ss68766273	A/C	CSHL-HAPMAP	HapMap-CEU	NA12891	CEPH1463.15	chr1-HapMap-CEU

Genotype data submitted for	1247	samples from	1247	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
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .