Reference SNP(refSNP) Cluster Report: rs1169538

Reference SNP(refSNP) Cluster Report: rs1169538

refSNP ID: rs1169538
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
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 ss1596652 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1169538 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
ss1596652	KWOK\|OVLP-000925-313680	fwd/B	C/T	gtttacatagttgtatatcaaatttggttt	agaaataaattatacagtaaatttaaaaat	10/04/00	10/10/03	87	Genomic	99 %
ss3705494	SC_JCM\|AC023817.3_59920	rev/T	A/G	atttttaaatttactgtataatttatttct	aaaccaaatttgatatacaactatgtaaac	09/25/01	10/10/03	100	Genomic	unknown
ss6862417	WI_SSAHASNP\|NT_034819.1_253230	fwd/B	C/T	gtttacatagttgtatatcaaatttggttt	agaaataaattatacagtaaatttaaaaat	02/12/03	10/10/03	111	Genomic	unknown

Fasta sequence (Legend)

 TTTTCTTTTT GTTACAATAT AGAGTGATGT TTCAAAACAC AAACATAATA GGTAGAGTCA
 ATTACTTAGG GGAGTCTAAA CCTGGAGGTA ACATTAGAAA TAGAAATAAT AAAATGCAGT
 GTTTTTGGAT TTGTCTGTTA AGATTATTTT AATCCAAATC ATATTTAATG GTTTACATAG
 TTGTATATCA AATTTGGTTT
 Y
 AGAAATAAAT TATACAGTAA ATTTAAAAAT GCAAAAAATG TATATTGTTA TACATTCTGT
 AACCTATGAA TCCATATAAC TTGGGCAAGa aaattatata attaaaaata aaaCCTTTCT
 GTTCTCAATT ATGTTTTAGG GACAGCTATA TAGTTCACAC TCACAAAGGA ATCATAAAAA
 CTCTATGTAT AATCTTGGAA GTAAAAATAT CTGTTGTATC ATAT

GeneView

GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1169538 was not linked to the human genome 36.3 because it aligned to more than 2 locations on the genome.

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838928.2	105327	21255505	minus	G	alt_assembly_8	HuRef	HuRef	view	200
5	NW_001838930.2	53233	34169340	plus	C	alt_assembly_8	HuRef	HuRef	view	200
5	NW_922640.1	84886	66040103	minus	G	alt_assembly_1	Celera	Celera	view	200
5	NT_006713.14	19561912	69003310	minus	G	ref_assembly	reference	reference	view	200
5	NT_006713.14	19772930	69214328	plus	C	ref_assembly	reference	reference	view	200
5	NT_006713.14	20141653	69583051	minus	G	ref_assembly	reference	reference	view	200
5	NT_113801.1	681325	69646692	minus	A	alt_assembly_5	c5_H2	c5_H2	view	200
5	NT_113801.1	893308	69858675	plus	T	alt_assembly_5	c5_H2	c5_H2	view	200
5	NT_006713.14	20438020	69879418	minus	A	ref_assembly	reference	reference	view	200
5	NT_006713.14	20648812	70090210	plus	C	ref_assembly	reference	reference	view	200
5	NT_006713.14	21141978	70583376	minus	G	ref_assembly	reference	reference	view	200
8	NT_113910.1	100281	unplaced	plus	C	ref_assembly	reference	reference	view	200
Un	NW_923221.1	1240	unplaced	plus	C	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AC023817 AC011244 AL161433 AL161433.3

dbSNP Blast Analysis
GenBank HTGS Draft:
AL161433.3

Population Diversity

There is no frequency data.

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .