Reference SNP(refSNP) Cluster Report: rs33267

Reference SNP(refSNP) Cluster Report: rs33267

refSNP ID: rs33267
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	76/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	T
Clinical Association:	unknown

HGVS Names
NM_016144.2:c.511-53671A>G
NT_034772.5:g.17988556A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2057714 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs33267 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
ss35602	KWOK\|OVLP-31553	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	04/28/00	10/10/03	76	Genomic	99 %
ss324218	KWOK\|OVLP-000621-32710	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	06/30/00	10/10/03	79	Genomic	99 %
ss1023020	KWOK\|OVLP-000804-307540	rev/T	A/G	ttaaatctctgatctgtactaatatcatca	ctcctactgagaattagaataacagtagaa	09/02/00	10/10/03	86	Genomic	97 %
ss1024003	KWOK\|OVLP-000804-315398	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	09/02/00	10/10/03	86	Genomic	97 %
ss1024348	KWOK\|OVLP-000804-318179	rev/T	A/G	ttaaatctctgatctgtactaatatcatca	ctcctactgagaattagaataacagtagaa	09/02/00	10/10/03	86	Genomic	97 %
ss2057714	KWOK\|OVLP-000925-638818	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	10/06/00	04/07/04	87	Genomic	97 %
ss4123865	SC_JCM\|AC018752.4_178252	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	10/15/01	10/10/03	101	Genomic	unknown
ss14668640	WI_SSAHASNP\|chr5.NT_034772.5_17988556	rev/T	A/G	ttaaatctctgatctgtactaatatcatca	ctcctactgagaattagaataacagtagaa	11/05/03	11/22/03	119	Genomic	unknown
ss22228960	SSAHASNP\|WGSA-200403-chr5.chr5.NT_034772.5_17988556	rev/T	A/G	ttaaatctctgatctgtactaatatcatca	ctcctactgagaattagaataacagtagaa	03/21/04	03/21/04	121	Genomic	unknown
ss24451671	PERLEGEN\|afd3592293	rev/T	A/G	ttaaatctctgatctgtactaatatcatca	ctcctactgagaattagaataacagtagaa	08/10/04	09/13/04	123	Genomic	unknown
ss44654315	ABI\|hCV622803	rev/T	A/G	ttaaatctctgatctgtactaatatcatca	ctcctactgagaattagaataacagtagaa	07/19/05	11/03/06	126	Genomic	unknown
ss66020035	AFFY\|SNP_A-1653193	rev/T	A/G	tctctgatctgtactaatatcatca	ctcctactgagaattagaataacag	10/26/06	10/26/06	127	Genomic	unknown
ss66616124	ILLUMINA\|HumanHap300v1.1_rs33267	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	11/09/06	11/09/06	127	Genomic	unknown
ss67294095	ILLUMINA\|HumanHap550v1.1_rs33267	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	11/14/06	11/14/06	127	Genomic	unknown
ss67698073	ILLUMINA\|HumanHap650Yv1.0_rs33267	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	11/14/06	11/14/06	127	Genomic	unknown
ss68946609	PERLEGEN\|PGP03592293	rev/T	A/G	ttaaatctctgatctgtactaatatcatca	ctcctactgagaattagaataacagtagaa	01/30/07	08/14/07	127	Genomic	unknown
ss70772705	ILLUMINA\|HumanHap550v3.0__rs33267	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	04/20/07	03/30/08	130	Genomic	unknown
ss71348225	ILLUMINA\|HumanHap650Yv3.0_rs33267	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	04/23/07	04/23/07	127	Genomic	unknown
ss75451047	ILLUMINA\|ILMN_Human_1M_rs33267	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	08/28/07	08/29/07	129	Genomic	unknown
ss77281125	HGSV\|Cor12156_SNV_20070510.chr5_115601442	rev/T	A/G	ttaaatctctgatctgtactaatatcatca	ctcctactgagaattagaataacagtagaa	10/09/07	10/12/07	129	Genomic	unknown
ss79160942	ILLUMINA\|HumanHap300v2.0_rs33267	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	04/18/07	11/18/07	130	Genomic	unknown
ss83356148	KRIBB_YJKIM\|KHS442263	fwd/B	C/T	ttctactgttattctaattctcagtaggag	tgatgatattagtacagatcagagatttaa	12/04/07	12/04/07	130	Genomic	unknown
ss93220101	BCMHGSC_JDW\|JWB-2027189	rev/T	A/G	ttaaatctctgatctgtactaatatcatca	ctcctactgagaattagaataacagtagaa	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATTGATTTCC AGATAATATA AATTTATTCA AAACAAAATA CTGTAACATT CTGGGAGCAG
 ATTGCTTTTA CTTTTATTAA ATTTACCTTT ATTACAACTA AGAAAATTGC TTTGCAACGA
 CGACATTCTG ACCCTTTAGC TTTGTTGTCA TTTAAAATCT TTCCCAAAGT TTCTACTGTT
 ATTCTAATTC TCAGTAGGAG
 Y
 TGATGATATT AGTACAGATC AGAGATTTAA GATTTAACAC CACTGCTAAC TTGCAAGAAA
 TACAAAATGC ATTTATTGCA TTTTATGAGC TTTGCTCATA ATTTAACCAT GATAATAAAA
 AGCAGATTAA AGATAATACC TGCTCATGTG AAATATTTCC TAAGAGTACT TCAGCTTAAA
 AATCTTGCCt cttttttttc tagaagcagg gtctcaatac gttgcccagg ctagcctcaa
 acttttgcgc tccagtgatc ctcccacctc agcctcccaa gtagctggac tatatagcat
 gtgccattgc gcttggcAAT TTTTTTTCTG TAACGTTTAT CTACATTTTA AAATAAAAGC
 TTGATGTAGT ATTTTTTTTC AAGTTTATGA ACTTATGATA GAACTAAATT GAAAATC

GeneView

GeneView via analysis of contig annotation: COMMD10 COMM domain containing 10

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_034772->NM_016144

function

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


reference	NT_034772->NM_016144->NP_057228	17988556	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs33267 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838952.2	23222300	110754408	plus	C	alt_assembly_8	HuRef	HuRef	view	200
5	NW_922751.1	16144247	111523076	minus	A	alt_assembly_1	Celera	Celera	view	200
5	NT_034772.5	17988556	115601442	minus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_034772 AC018752.4 AC022122.2 AC092318

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss2057714	AfAm	African American	10	IG		0.600	0.400	0.343	0.300		0.700

	Caucasian	European	22	IG	0.273	0.545	0.182	0.752	0.545		0.455

	Asian	Asian	12	IG	0.167	0.333	0.500	0.584	0.333		0.667

	CEPH	European	12	IG	0.500	0.333	0.167	0.584	0.667		0.333

	PDpanel	Global	44	IG	0.182	0.500	0.318	1.000	0.432		0.568

	HapMap-CEU	European	120	IG	0.283	0.433	0.283	0.317	0.500		0.500

	HapMap-HCB	Asian	90	IG	0.022	0.556	0.422	0.050	0.300		0.700

	HapMap-JPT	Asian	90	IG	0.022	0.356	0.622	0.527	0.200		0.800

	HapMap-YRI	Sub-Saharan African	118	IG		0.017	0.983	1.000	0.008		0.992

	CHMJ	Asian	74	IG					0.189	0.014	0.797

ss24451671	AFD_EUR_PANEL	European	48	IG	0.333	0.458	0.208	0.752	0.562		0.438

	AFD_AFR_PANEL	African American	46	IG		0.478	0.522	0.150	0.239		0.761

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.208	0.708	0.150	0.188		0.812

ss44654315	AoD_African_American		90	AF					0.140		0.860

	AoD_Caucasian		92	AF					0.560		0.440

	AoD_Chinese		90	AF					0.170		0.830

	AoD_Japanese		90	AF					0.220		0.780

ss68946609	HapMap-CEU	European	120	GF	0.283	0.433	0.283		0.500		0.500

	HapMap-HCB	Asian	90	GF	0.022	0.556	0.422		0.300		0.700

	HapMap-JPT	Asian	90	GF	0.022	0.356	0.622		0.200		0.800

	HapMap-YRI	Sub-Saharan African	120	GF		0.017	0.983		0.008		0.992

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss2057714	319	37	103	178
ss24451671	71
ss68946609	269

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs33267	377	37	103	178

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5142	ss2057714	T/T	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	r23_ch5_YRI_illumina:infinium_genotyping_2.0.0	48190
5142	ss68946609	A/G	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	chr5-HapMap-YRI

Genotype data submitted for	391	samples from	377	individuals	Individual with multiple genotypes submission:	275

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .