Reference SNP(refSNP) Cluster Report: rs233453

Reference SNP(refSNP) Cluster Report: rs233453

refSNP ID: rs233453
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

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

HGVS Names
NM_015202.1:c.311-137A>G
NT_010393.15:g.18955328A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16696495 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs233453 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
ss301569	KWOK\|OVLP-000621-320512	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	06/30/00	10/10/03	79	Genomic	97 %
ss587272	SC_JCM\|AC002551.1_84468	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	07/12/00	10/10/03	80	Genomic	unknown
ss1052910	KWOK\|OVLP-000804-67862	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	09/02/00	10/10/03	86	Genomic	94 %
ss1973910	KWOK\|OVLP-000925-543692	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	10/06/00	10/10/03	87	Genomic	94 %
ss12353860	WI_SSAHASNP\|chr16.NT_010393.13_18915287	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	07/04/03	10/10/03	116	Genomic	unknown
ss16696495	CSHL-HAPMAP\|CSHL-HuAA-200402.chr16.NT_010393.14_18954402	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	02/17/04	05/16/04	120	Genomic	unknown
ss24463998	PERLEGEN\|afd4160951	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	08/10/04	09/13/04	123	Genomic	unknown
ss43842621	ABI\|hCV3248920	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	07/18/05	07/18/05	126	Genomic	unknown
ss75163458	ILLUMINA\|ILMN_Human_1M_rs233453	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	08/28/07	08/29/07	129	Genomic	unknown
ss78421207	HGSV\|Cor12878_SNV_20070510.chr16_27549750	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	10/17/07	10/19/07	129	Genomic	unknown
ss79038565	HGSV\|Cor18507_SNV_20070510.chr16_27549750	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	10/19/07	10/21/07	129	Genomic	unknown
ss90359488	BCMHGSC_JDW\|JWB-0935696	fwd/T	A/G	cttgttttctgatgtcttgttgccacaacc	cgctgtagtcaatgtcctcatacacaagac	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 CAGAGTGTAG CTTGAGCTCC CCAGCCCCCA GGGCAAATAG GGAAACCAGT GGCTCTCCTA
 GTTTTCACAG TGGAGGCAGA CCTGCTGCTG CTAGTAAGGA GAATTCAGCT TTTCCTGGTC
 CAGGTTTCAG GGAGGAACAG ATAACAGGAT TCTGTGTACT TGGAACACCA GCAGTACCtt
 cattcattca ttcattcatt caGCAAAGAG ATTCACCCTC TACACTCTTT TACACAAATG
 GTGACCTCTT GTACCTACTG TCCTGAACCT TGTCTCTGTA GCTTAGAGAC TCTTCTCTGT
 ATATACAGAC CTGCCTGATC CGGCCATATA TTATACATAT TATTCCATGG CATGGATATA
 TATACTGGAA CTTATTTACC CATTCCTTTT TTGCTCAACA TTTAGCTTGT TTTCTGATGT
 CTTGTTGCCA CAACC
 R
 CGCTGTAGTC AATGTCCTCA TACACAAGAC TTTGGGCACA CTGATACGCA TTTTAGACAT
 GAGTTACAAA CCAACCCAGT ACTGTGAGCT TGTCATCAGT GCCTCACCAA GTCTCCTTCC
 CTCGTCTCTG GTGCAGATTA TGGACGAAGA ACTCTGTTTC GAGAAGCTGA AGAAGCCTTA
 AGACGCAGTT CACGGACAGC CCCCAGTAAA GTCCAGCGCC GAGGATGGCA CCAGGTCTGG
 AGACT

GeneView

GeneView via analysis of contig annotation: KIAA0556 KIAA0556

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_010393->NM_015202

function

HuRef

NW_001838401->NM_015202

function

Celera

NW_926217->NM_015202

function

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


reference	NT_010393->NM_015202->NP_056017	18955328	forward	intron

HuRef	NW_001838401->NM_015202->NP_056017	4170400	forward	intron

Celera	NW_926217->NM_015202->NP_056017	4939784	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs233453 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_001838401.1	4170400	25730641	plus	A	alt_assembly_8	HuRef	HuRef	view	435
16	NW_926217.1	4939784	26419580	plus	A	alt_assembly_1	Celera	Celera	view	435
16	NT_010393.15	18955328	27549750	plus	A	ref_assembly	reference	reference	view	435

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010393 AC016597 AC016597.4

dbSNP Blast Analysis
GenBank HTGS Finished:
AC002551.1 AC016597.4 NC_000016.8

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss16696495	CEPH		184	AF					0.270	0.730

	HapMap-CEU	European	120	IG		0.317	0.683	0.150	0.158	0.842

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG			1.000			1.000

ss24463998	AFD_EUR_PANEL	European	48	IG	0.042	0.250	0.708	0.655	0.167	0.833

	AFD_AFR_PANEL	African American	46	IG		0.043	0.957	1.000	0.022	0.978

	AFD_CHN_PANEL	Asian	48	IG			1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.095+/-0.196	332	260	9	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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .