Reference SNP(refSNP) Cluster Report: rs13177884

Reference SNP(refSNP) Cluster Report: rs13177884

refSNP ID: rs13177884
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	121/129
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
NM_031900.1:c.363-1008G>A
NT_006576.15:g.35010935C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss42572806 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs13177884 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
ss22317126	SSAHASNP\|WGSA-200403-chr5.chr5.NT_006576.14_17490284	fwd/B	C/T	accagattatacagatttctttactacaga	attttagtacctataatagactagtgtacg	03/21/04	03/21/04	121	Genomic	unknown
ss42572806	ABI\|hCV3206790	fwd/B	C/T	accagattatacagatttctttactacaga	attttagtacctataatagactagtgtacg	07/18/05	11/03/06	126	Genomic	unknown
ss93058484	BCMHGSC_JDW\|JWB-1962565	fwd/B	C/T	accagattatacagatttctttactacaga	attttagtacctataatagactagtgtacg	02/26/08	03/03/08	129	Genomic	unknown

Fasta sequence (Legend)

 GTGTGGATGA ATATTTTGTA ACTATAAAGC CACATTCTTT GAAAGATTGG GCCAACCTTA
 CAGGATTAGA AGGTTCATAC TGAGAGATAA TAGGGGCTAA GGATGACAGA TTTGTGGAAC
 CTGACTTGGC TTTGAAAACA CAAACCAAGT TGTCTGAACT TGCTGTAAAG GACATTAATT
 GCTACAGTTT GTTACAGGCC AATTTTATTT GCTGTTAATA TCTTTCACAT CAGAAAAAAA
 TCAATTTAGT GGGTAAATAT TTTGAGAAAT ACCAGATTAT ACAGATTTCT TTACTACAGA
 Y
 ATTTTAGTAC CTATAATAGA CTAGTGTACG CTGTTTCTCT TCAGAAGGGA GATATAGTTT
 AAAGTGTTTC CCAAACTTAT TTTCTCATGG GACCCTTTTC CACGGAAACT CCTGTGATCA
 GTGTTCCATG AAACTCACTT TAGAAAATTG TGGAGTATCA GTAAATCCTT GAAAAGAAGA
 GACATTTGAC AAAAACATTG TTTAGCAAAA TATATGAGAG TCACAGGAGG GGTAGAAAAG
 ATGGCCTCCC ATTTCCAGGG AAGACTGTCA ATGTTACTGG GAAGATTCAG TGAGAATGTT

GeneView

GeneView via analysis of contig annotation: AGXT2 alanine-glyoxylate aminotransferase 2

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_006576->NM_031900

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_006576->NM_031900->NP_114106	35010935	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs13177884 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_922596.1	630871	34920357	plus	C	alt_assembly_1	Celera	Celera	view	300
5	NW_001838932.2	670365	34986925	minus	A	alt_assembly_8	HuRef	HuRef	view	300
5	NT_006576.15	35010935	35073935	plus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_006576

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	T
ss42572806	HapMap-CEU	European	112	IG	0.482	0.357	0.161	0.150	0.661	0.339

	HapMap-HCB	Asian	84	IG	0.786	0.214		0.439	0.893	0.107

	HapMap-JPT	Asian	86	IG	0.744	0.256			0.872	0.128

	HapMap-YRI	Sub-Saharan African	116	IG	0.879	0.121		0.655	0.940	0.060

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.273+/-0.249	270	210	0	0

Validation Summary:

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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .