Reference SNP(refSNP) Cluster Report: rs1557508

Reference SNP(refSNP) Cluster Report: rs1557508

refSNP ID: rs1557508
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	88/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001080485.1:c.*269A>G
NT_011726.13:g.3434176A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss84824374 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1557508 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
ss2400891	TSC-CSHL\|TSC0444744	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	10/20/00	04/07/04	88	Genomic	95 %
ss8259032	SC_SNP\|NT_011726.8_2948646	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	04/17/03	10/10/03	114	Genomic	unknown
ss21012241	SSAHASNP\|WGSA-200403-chrX.chrX.NT_011726.11_3287126	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	03/19/04	03/19/04	121	Genomic	unknown
ss43537805	ABI\|hCV2609393	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	07/18/05	07/18/05	126	Genomic	unknown
ss65722212	ILLUMINA\|Human1-rs1557508	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	10/10/06	10/10/06	127	Genomic	unknown
ss71641688	SI_EXO\|NT_011726.13_3434176	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	05/07/07	05/07/07	127	Genomic	unknown
ss75007605	ILLUMINA\|ILMN_Human_1M_rs1557508	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	08/28/07	08/29/07	129	Genomic	unknown
ss84824374	HGSV\|Cor19240_SNV_20070510.chrX_152097992	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	11/30/07	12/08/07	130	Genomic	unknown
ss86011579	HGSV\|Cor18956_SNV_20070510.chrX_152097992	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	11/30/07	12/10/07	130	Genomic	unknown
ss94438651	BCMHGSC_JDW\|JWB-2713863	fwd/T	A/G	atgccttgaatccaagaatgagagaggaca	atctggatgtggggtagggaggggcttaga	02/26/08	03/06/08	129	Genomic	unknown

Fasta sequence (Legend)

 AGGCCTTCCG CCGGAGCTCC GGCCTCAGTC GCCACCGGCG GATCCACAGT GGGGCGCGGC
 GCTGCGAATG CAGCCAGTGT GGCCGCGTGT TCAAGAGGCG CTCGGCACTG CAGAAGCATC
 AGCCAACCCA CCACGAGTAG AAACGCCCTG TGGTCCCGCG GGACAGGGAC GGAGTCCCCA
 GAGGGGATGG CAGAGTCAAA GGAGATGAAC AGTTTTGTAG CGCTTATATA TTTTGTCTTC
 CAAAAGGTTG AGACCGATTT ATACTGCCAC CAGCAATTTA TAAGTGTTAC GTTATGCCCA
 TCAAGAGTAG CTTGTACCAT TTAACTTAGT TTGGCTAGTT TAACTGGTAG GAAGTACCAT
 CAAGGTATTT CAGTCCACAT GCCTTGAATC CAAGAATGAG AGAGGACA
 R
 ATCTGGATGT GGGGTAGGGA GGGGCTTAGA GGTCATCAAC TCCAAGCTCC CCCCGCCCCA
 GAGAAACACA CAGAGCTGTT CCACGATGGC GTCCTCATAA TGTGATCCCA GCTTTCCTGA
 AGAGAACGTT GCCCTCATGA TTTTTGGCCT ACTTGAATTT ATAAATTTTT AGGGATGTAA
 ATAGAACACT CAAATGTCTT AAAATATTTA ATTTATTAAT TTAGTTATAC ATACATACTG
 TAAATCACAT ATTATATAAA ATAATATATT AATTTAGAAA ATACCCCATT TTTGCCACCC
 TCCCTTTCAC GAAATCATTT TACTCTGACT CCTCACCGTC TTCACCAACA TGGGAACCCT
 GTTTGAGTCA TCAGACAGTT TCAAGACACA CCCAGTCACT TCCATCCGAG CTCTGCACGG
 TCGCTCAGTG ACGATCCCTT CATGAGGCTC TCATTAGAAA TTTTCTCCCA AGCCATAAGA
 CCATATTTGC AGAACATTAG

GeneView

GeneView via analysis of contig annotation: ZNF275 zinc finger protein 275

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_011726->NM_001080485

function

HuRef

NW_001842416->NM_001080485

function

Celera

NW_927732->NM_001080485

function

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


reference	NT_011726->NM_001080485->	3434176	forward	1727	3' UTR

HuRef	NW_001842416->NM_001080485->	13714	reverse	1728	3' UTR

Celera	NW_927732->NM_001080485->	554268	forward	1728	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1557508 maps exactly once on NCBI human chromosome X

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
X	NW_001842416.2	13714	141272985	minus	C	alt_assembly_8	HuRef	HuRef	view	364
X	NT_011726.13	3434176	152266896	plus	A	ref_assembly	reference	reference	view	364
X	NW_927732.1	554268	152846621	plus	G	alt_assembly_1	Celera	Celera	view	364

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011726.13

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_001080485.1	AC152007.1 AC152008.1 AC153069.1 NC_000023.9

UniGene Cluster ID
348963

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss2400891	HapMap-CEU	European	120	IG	0.433	0.217	0.350	0.479	0.542	0.458

	HapMap-HCB	Asian	90	IG	0.156	0.178	0.667	1.000	0.244	0.756

	HapMap-JPT	Asian	88	IG	0.091	0.023	0.886	0.020	0.102	0.898

	HapMap-YRI	Sub-Saharan African	120	IG	0.100	0.133	0.767	0.273	0.167	0.833

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.401+/-0.199	270	210	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .