Reference SNP(refSNP) Cluster Report: rs3793405

Reference SNP(refSNP) Cluster Report: rs3793405

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/130
Map to Genome Build:	36.3

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

HGVS Names
NM_019851.1:c.346G>C
NP_062825.1:p.Gly116Arg
NT_030737.9:g.4698227C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss28476571 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3793405 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
ss4979779	YUSUKE\|IMS-JST150914	fwd/B	C/G	ctcctttgtcattcattccaagatagagac	actgtccacacctctaatactgaccagtcc	08/12/02	10/10/03	107	Genomic	unknown
ss28476571	EGP_SNPS\|FGF20-008414	rev/T	C/G	ggactggtcagtattagaggtgtggacagt	gtctctatcttggaatgaatgacaaaggag	07/27/04	11/02/06	126	Genomic	unknown
ss69041768	PERLEGEN\|PGP04775928	fwd/	C/G	ctcctttgtcattcattccaagatagagac	actgtccacacctctaatactgaccagtcc	01/30/07	03/31/08	127	Genomic	unknown
ss74820882	AFFY\|SNP_M-324250	fwd/B	C/G	ctcctttgtcattcattccaagatagagac	actgtccacacctctaatactgaccagtcc	08/09/07	08/09/07	128	Genomic	unknown
ss74892049	ILLUMINA\|ILMN_Human_1M_rs3793405	fwd/	C/G	ctcctttgtcattcattccaagatagagac	actgtccacacctctaatactgaccagtcc	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 AAGGTAATAA TGGTTGGGGG TTTTAAAAAT ATAATTGAGT TACTATACTA TTGCCCAGAC
 ACATGGAAAT TTAGCAGGAT AGATTTCAAT TTCTACGTAA GTATGTTTTA TATACTTCTA
 CCAGACATTC TTGGTAGACA TTTTAATTAC ATAATAGATA GTCAATATTT TAAGAATTAC
 AATAATAATA AAAAATAAAA ATAATACGTA CTGATCCATA GAGTTCTCCT TTGTCATTCA
 TTCCAAGATA GAGAC
 S
 ACTGTCCACA CCTCTAATAC TGACCAGTCC CACTGCCACA CTGATGAATT CCAAGATACC
 TGCATATGTA AACAATTCAT AAAAACACCA TGTTTTGTAT TTATGCATGA GCATATGACT
 AACAAAAATC TTCCAAATAG TAGCGGTAGT CGGCCATTAT TGCCAAATAT AATGATGTAC
 GTGTAAAAGT CCTTTGTACA CTGGAAACAG CTATGCAATT GTTTTATGAC AGATGAAAAA
 AGGACAAAAA AGGAA

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_023737.1

dbSNP Blast Analysis

UniGene Cluster ID
199905

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss28476571	PDR90	Global	180	IG	0.989	0.011		1.000	0.994	0.006

	HapMap-CEU	European	120	IG	0.983	0.017		1.000	0.992	0.008

	HapMap-HCB	Asian	90	IG	0.956	0.044		1.000	0.978	0.022

	HapMap-JPT	Asian	90	IG	0.933	0.044	0.022		0.956	0.044

	HapMap-YRI	Sub-Saharan African	118	IG	1.000				1.000

ss69041768	HapMap-CEU	European	120	GF	1.000				1.000

	HapMap-HCB	Asian	90	GF	0.956	0.044			0.978	0.022

	HapMap-JPT	Asian	90	GF	0.933	0.044	0.022		0.956	0.044

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss28476571	613	1	5	350

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs3793405	615	1	5	350

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
171	ss28476571	C/G	CSHL-HAPMAP	HapMap-CEU	NA07022	CEPH1340.11	r27_ch8_CEU_perlegen:genotyping_1.0.0	3724692
5271	ss28476571	C/G	CSHL-HAPMAP	HapMap-YRI	NA19103	YOR042.01	r27_ch8_YRI_perlegen:genotyping_1.0.0	3724692

Genotype data submitted for	615	samples from	615	individuals	Individual with multiple genotypes submission:	0

Validation Summary:

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

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Revised: May 25, 2006 1:38 PM .