Reference SNP(refSNP) Cluster Report: rs1064697

Reference SNP(refSNP) Cluster Report: rs1064697

refSNP ID: rs1064697
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss12694644 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1064697 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
ss1553581	LEE\|1380701	fwd/T	A/G	tgacacattcaaagaagaactttctgcccc	gctttgcaggatgaaaagctttccctcctg	09/13/00	10/10/03	86	cDNA	unknown
ss12694644	SI_MHC_SNP\|AL713966.7_112992_CT	rev/B	C/T	caagcaggaaagcttttcatcctgcaaagc	ggggcagaaagttcttccttgaatgtggtc	09/10/03	05/25/07	128	Genomic	unknown
ss50395356	UWGC\|HLA-131812	fwd/T	A/G	tgacacattcaaagaagaactttctgcccc	gctttgcaggatgaaaagctttccctcctg	02/02/06	11/03/06	128	Genomic	unknown

Fasta sequence (Legend)

 TTAAGAGCTG TAACACTCAC TGTGAAGGTC TGCAGGAAGT CAGCGAGACC ACAAACCCAC
 CGGAAGGAAC AAACTCAGGA CACACCAGAA TGATGGTAGA GGTGATAAGG CATGAGACAG
 AAATAATAGG AAAGACTTTG GATCCAAATT TCTGATCAGG CAATTTACAC CAAAATTCCT
 CCTCTCCACT TAGAAAAGGT GTGCTCTGCG GGACTATTGG CTCAGGGGAG ACTCAGGAAC
 TTCTTTTTCT TCTTCCTGCA GTGCTCTCAT CTGAGCCCTT GAAAGAGGGG AAAAGAAACT
 GTTAGTAGAG CCAGGTTGAA AACAACACTC TCCTCTGTCT TTTGCAGGAT TCCTGAGCTG
 AAATGCAGAT GACCACATTC AAGGAAGAAC TTTCTGCCCC
 R
 GCTTTGCAGG ATGAAAAGCT TTCCTGCTTG GCAGTTATTC TTCCACAAGA GAGGGCTTTC
 TCAGGACCTG GTTGCTACTG GTTCGGCAAC TGCAGAAAAT GTCCTCCCTT GTGGCTTCCT
 CAGCTCCTGC CCTTGGCCTG AAGTCCCAGC ATTGATGGCA GCGCCTCATC TTCAACTTTT
 GTGCTCCCCT TTGCCTAAAC CGTATGGCCT CCCGTGCATC TGTATTCACC CTGTATGACA
 AACACATTAC ATTATTAAAT GTTTCTCAAA GATGGAGTTA AATATCATCT GGTCCATTTG
 GCTCCAAAGA CAGAAAATGA AAAGAAAAAG GGAAGATTAT TTTCCAATAG AATAATGATT
 TTCATGTATA TGTCATGAGT GTGTGAGGTA ATGCGTATGT

GeneView

GeneView via analysis of contig annotation: LOC730415 hypothetical protein LOC730415

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: HLA-DRB4 major histocompatibility complex, class II, DR beta 4

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

Celera

NW_923073->XM_001124749

function

c6_QBL

NT_113896->XM_001723414

function

c6_QBL

NT_113896->XM_001723417

function

c6_QBL

NT_113896->XM_001723419

function

HuRef

NW_001841135->NM_021983

function

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


Celera	NW_923073->XM_001124749->	5559651	reverse	944	3' UTR

c6_QBL	NT_113896->XM_001723414->	415845	reverse	944	3' UTR

c6_QBL	NT_113896->XM_001723417->	415845	reverse	942	3' UTR

c6_QBL	NT_113896->XM_001723419->	415845	reverse	920	3' UTR

HuRef	NW_001841135->NM_021983->NP_068818	104018	reverse		intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: See all two hits of rs1064697 on the NCBI human genome map
!WARNING: Several map positions found! The map position is found by blasting with the contig sequences.

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NG_002433.1	87762	32446180	minus	T	alt_haplotype_7	DR53	DR53	view	50
6	NT_113891.1	3934942	32623485	minus	T	alt_assembly_3	c6_COX	c6_COX	view	50
6	NT_113896.1	415845	32624340	minus	T	alt_assembly_4	c6_QBL	c6_QBL	view	50
6	NT_007592.14	23379033	32628761	minus	T	ref_assembly	reference	reference	view	50
6	NT_007592.14	23405078	32654806	minus	C	ref_assembly	reference	reference	view	50
6	NW_923073.1	5559651	34095330	minus	T	alt_assembly_1	Celera	Celera	view	50
Un	NW_001841135.1	104018	unplaced	minus	T	alt_assembly_8	HuRef	HuRef	view	50

NCBI Resource Links

Submitter-Referenced
GenBank
M20430 Hs.181366

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank STS:	GenBank mRNA:
NM_021983.4 XM_001124749.1	AL662842.3 AL929581.5 Z84489.1	BV179155.1	AK290388.1 AK291499.1 AK293020.1 BC007920.2 BC008403.1 BC031023.1 M11867.1 U83583.1 U83584.1 X00699.1

UniGene Cluster ID
520049

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss50395356	HLA_PANEL	multiple	6	IG	0.333	0.667		0.667	0.333

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.444+/-0.157	0	0	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 .