Reference SNP(refSNP) Cluster Report: rs5742973

Reference SNP(refSNP) Cluster Report: rs5742973

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	114/130
Map to Genome Build:	36.3

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

HGVS Names
NG_008648.1:g.12804G>C
NM_000534.3:c.79G>C
NM_000534.4:c.79G>C
NM_001128143.1:c.79G>C
NM_001128144.1:c.79G>C
NP_000525.1:p.Glu27Gln
NP_001121615.1:p.Glu27Gln
NP_001121616.1:p.Glu27Gln
NT_005403.16:g.40866031G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss7986716 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5742973 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss7986716	EGP_SNPS\|PMS1-019321		fwd/T	C/G	atcatcacttcggtggtcagtgttgtaaaa	agcttattgaaaactccttggatgctggtg	04/04/03	01/23/04	114	Genomic			unknown
ss74879162	ILLUMINA\|ILMN_Human_1M_rs5742973		fwd/	C/G	atcatcacttcggtggtcagtgttgtaaaa	agcttattgaaaactccttggatgctggtg	08/28/07	08/29/07	129	Genomic			unknown

Fasta sequence (Legend)

 NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN NNNNNNNNNN
 NNNNNNNGAT CTATTTTCAT CTGTCATTAT TATTGCCATT TGTCCTGTTG GTCAGGAATG
 CTTAACAATT CTTACAAGTT GCATTTTTAT CTTCTAGCTG CTCTGTTAAA AGCGAAAATG
 AAACAATTGC CTGCGGCAAC AGTTCGACTC CTTTCAAGTT CTCAGATCAT CACTTCGGTG
 GTCAGTGTTG TAAAA
 S
 AGCTTATTGA AAACTCCTTG GATGCTGGTG CCACAAGCGT AGATGTTAAA CTGGTGAGTG
 TCCTTGAGAA CCCAAATACC TTTAAGACAA AGAAAAGGGT CTGGACACAT GTTTTCTCCT
 TAAACTGTTA CCTTTATTTT ATTTCTTTAC ACCAATAAAT TATTCTTAGG ACATTGGACC
 CTTTGTCTTA AGAGTAAATC Cttaaaaata aattttaatt taaattaaCA TTATAGTAAC
 ACTAAAGGAA ATATA

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
AY267352

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/G	G/G	HWP	C	G
ss7986716	PDR90	Global	168	IG	0.012	0.988	1.000	0.006	0.994

	HapMap-CEU	European	116	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	88	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.003+/-0.041	615	499	0	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 .