Reference SNP(refSNP) Cluster Report: rs4134833

Reference SNP(refSNP) Cluster Report: rs4134833

refSNP ID: rs4134833
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	108/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_020196.2:c.523-87G>A
NT_077812.2:g.295239C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss5587048 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4134833 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
ss5587048	EGP_SNPS\|HCNP-004404		fwd/T	A/G	gcttttgcccaagacactcataaatgggtg	ggggggacgccccgaagccactgaatcggg	09/27/02	04/07/04	108	Genomic			unknown
ss12469220	WI_SSAHASNP\|chr19.NT_077812.1_295239		rev/B	C/T	cccgattcagtggcttcggggcgtcccccc	cacccatttatgagtgtcttgggcaaaagc	07/04/03	10/10/03	116	Genomic			unknown

Fasta sequence (Legend)

 AAGGCTGGAC CATTGGGGCT GAGACTGGAC CACCGCAGTC AAGGCTGTGC CCTTGCGGGT
 CAAGGCTAAC CCAAAAAGTC CACAGCTGGT CTAGTCAGGA CTGAGGCTGG ACCAGTGGAG
 CCAAGGCAGG ACCCACAGGG GGTTGAGCCT AACCCAGTGG GGCCAAGGCT AGACCAGTAG
 GAACCGGGCT GGACCAGTGG GGCTGAGGCT GGTTTGACAG GGCTTGCTTT TGCCCAAGAC
 ACTCATAAAT GGGTG
 R
 GGGGGGACGC CCCGAAGCCA CTGAATCGGG AGGTGGGCGT AGCCCTGCCA CCCCACTGAC
 TGCCTGAGGG GTGGCTCGGT CCCCAGCTGA GTCCTGAGAG TGCAGAGGAG TACATTGAGT
 ACCTCAAGTC AAGTGACCGG CTGGATGAGG CCGCCCAGCG CCTGGCCACC GTGGTGAACG
 ACGAGCGTTT CGTGTCTAAG GCCGGCAAGT CCAACTACCA GGTGGGCCTG CCGGGAGCCG
 GCAACTGGGT GGGAG

GeneView

GeneView via analysis of contig annotation: XAB2 XPA binding protein 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_077812->NM_020196

function

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


reference	NT_077812->NM_020196->NP_064581	295239	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4134833 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838480.2	985698	7360911	plus	G	alt_assembly_8	HuRef	HuRef	view	255
19	NW_927173.1	6821151	7562427	minus	C	alt_assembly_1	Celera	Celera	view	255
19	NT_077812.2	295239	7597243	minus	C	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
NT_077812

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss5587048	PDR90	Global	180	IG	0.056	0.944	1.000	0.028	0.972

	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	88	IG		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.021+/-0.100	270	240	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 .