Reference SNP(refSNP) Cluster Report: rs2233901

Reference SNP(refSNP) Cluster Report: rs2233901

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	98/130
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_003008.2:c.821G>A
NP_002999.1:p.Ser274Asn
NT_011362.9:g.8904009G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8337938 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2233901 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
ss3181390	GENAISSANCE\|GEN3073	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	07/19/01	10/10/03	98	Genomic	unknown
ss4399020	LEE\|ge813200	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	04/25/02	10/10/03	106	cDNA	unknown
ss4428406	LEE\|e813199	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	04/26/02	10/10/03	106	cDNA	unknown
ss8337938	SC_SNP\|NT_011362.7_8904008	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	04/17/03	04/07/04	114	Genomic	unknown
ss16259996	CGAP-GAI\|1520177	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	11/18/03	11/22/03	120	cDNA	unknown
ss21768498	SSAHASNP\|WGSA-200403-chr20.chr20.NT_011362.8_8904009	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	03/20/04	03/20/04	121	Genomic	unknown
ss24695221	PERLEGEN\|afd4592596	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	08/10/04	09/13/04	123	Genomic	unknown
ss41438925	ABI\|hCV25618981	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	07/17/05	07/17/05	126	Genomic	unknown
ss66259129	AFFY\|SNP_A-4289137	fwd/T	A/G	cagacaaaaaatctca	tcaagatcaagagcat	10/27/06	08/14/07	127	Genomic	unknown
ss69242432	PERLEGEN\|PGP04592596	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	01/30/07	08/14/07	127	Genomic	unknown
ss74896873	ILLUMINA\|ILMN_Human_1M_rs2233901	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	08/28/07	08/29/07	129	Genomic	unknown
ss76404310	AFFY\|AFFY_6_1M_SNP_A-4289137	fwd/T	A/G	cagacaaaaaatctca	tcaagatcaagagcat	08/28/07	08/30/07	130	Genomic	unknown
ss81731493	KRIBB_YJKIM\|KHS131974	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	11/30/07	12/01/07	130	Genomic	unknown
ss86237038	CORNELL\|hCV11187323	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	01/21/08	01/21/08	129	Genomic	unknown
ss91707670	BCMHGSC_JDW\|JWB-1445417	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	02/26/08	03/02/08	129	Genomic	unknown
ss96231131	HUMANGENOME_JCVI\|1103643207535	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	03/25/08	03/25/08	130	Genomic	unknown
ss117555314	ILLUMINA-UK\|NA18507_000051816_NCBI36.1_chr20_43284508	fwd/T	A/G	acaagaatcaacaccagacaaaaaatctca	tcaagatcaagagcatggccggaaggcaca	01/19/09	01/19/09	130	Genomic	99 %

Fasta sequence (Legend)

 AATCCTTCTC AAGATCAGGG GAATAGCCCA TCTGGAAAGG GATTATCCAG TCAATGTTCA
 AACACAGAAA AAAGGCTATG GGTTCATGGA CTAAGTAAAG AACAAGCTTC AGCCTCTGGT
 GCACAAAAAG GTAGAACACA AGGTGGATCC CAAAGCAGTT ATGTTCTCCA AACTGAAGAA
 CTAGTAGTTA ACAAACAACA ACGTGAGACT AAAAATTCTC ATCAAAATAA AGGGCATTAC
 CAAAATGTGG TTGACGTGAG AGAGGAACAT TCAAGTAAAC TACAAACTTC ACTCCATCCT
 GCACATCAAG ACAGACTCCA ACATGGACCC AAAGACATTT TTACTACCCA AGATGAGCTC
 CTAGTATATA ACAAGAATCA ACACCAGACA AAAAATCTCA
 R
 TCAAGATCAA GAGCATGGCC GGAAGGCACA TAAAATATCA TACCCGTCTT CACGTACAGA
 AGAAAGACAA CTTCACCATG GAGAAAAGAG TGTACAGAAA GATGTATCCA AAGGCAGCAT
 TTCTATCCAA ACTGAAGAGA AAATACATGG CAAGTCTCAA AACCAGGTAA CAATTCATAG
 TCAAGATCAA GAGCATGGCC ATAAGGAAAA TAAAATATCA TACCAATCTT CAAGTACAGA
 AGAAAGACAT CTCAACTGTG GAGAAAAGGG CATCCAGAAA GGTGTATCCA AAGGCAGTAT
 TTCGATCCAA ACTGAAGAGC AAATACATGG CAAGTCTCAA AACCAGGTAA GAATTCCTAG
 TCAAGCTCAA GAGTATGGCC ATAAGGAAAA TAAAATATCA

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
Z47556.1 ABBA01052657 AI732134 Hs.180016

dbSNP Blast Analysis

UniGene Cluster ID
537218

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24695221	AFD_EUR_PANEL	European	48	IG	0.125	0.250	0.625	0.150	0.250	0.750

	AFD_AFR_PANEL	African American	44	IG		0.318	0.682	0.403	0.159	0.841

	AFD_CHN_PANEL	Asian	48	IG		0.125	0.875	0.752	0.062	0.938

ss66259129	HapMap-CEU	European	118	GF		0.254	0.746		0.127	0.873

	HapMap-HCB	Asian	90	GF		0.022	0.978		0.011	0.989

	HapMap-JPT	Asian	90	GF		0.022	0.978		0.011	0.989

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.150	0.833		0.092	0.908

ss69242432	HapMap-CEU	European	120	GF		0.267	0.733		0.133	0.867

	HapMap-HCB	Asian	90	GF			1.000			1.000

	HapMap-JPT	Asian	90	GF		0.022	0.978		0.011	0.989

	HapMap-YRI	Sub-Saharan African	120	GF		0.183	0.817		0.092	0.908

ss76404310	ICMHP		10	IG	0.200	0.200	0.600		0.300	0.700

ss8337938	CEPH		184	AF					0.110	0.890

	HapMap-CEU	European	120	IG		0.267	0.733	0.251	0.133	0.867

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	88	IG		0.023	0.977	1.000	0.011	0.989

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.217	0.750	0.403	0.142	0.858

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss24695221	71	3	16	51
ss66259129	256	2	34	220
ss76404310	5	1	1	3
ss8337938	1104	17	223	821
ss96231131	1		1

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs2233901	1179	19	240	889

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5133	ss8337938	N/N	CSHL-HAPMAP	HapMap-YRI	NA18502	YOR004.02	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5133	ss66259129	A/A	CSHL-HAPMAP	HapMap-YRI	NA18502	YOR004.02	chr20-HapMap-YRI
5142	ss8337938	N/N	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5142	ss66259129	G/G	CSHL-HAPMAP	HapMap-YRI	NA19194	YOR112.01	chr20-HapMap-YRI
5144	ss8337938	N/N	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5144	ss66259129	G/G	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	chr20-HapMap-YRI
5166	ss8337938	A/G	CSHL-HAPMAP	HapMap-HCB	NA18552	CH18552	r27_ch20_CHB_affymetrix:genomewidesnp_6.0	891007
5166	ss66259129	A/G	CSHL-HAPMAP	HapMap-HCB	NA18552	CH18552	chr20-HapMap-HCB
5240	ss8337938	A/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5240	ss66259129	G/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	chr20-HapMap-YRI
5259	ss8337938	A/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5259	ss66259129	G/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	chr20-HapMap-YRI
5260	ss8337938	A/G	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5260	ss66259129	G/G	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	chr20-HapMap-YRI
5268	ss8337938	N/N	CSHL-HAPMAP	HapMap-YRI	NA19094	YOR040.01	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5268	ss66259129	A/G	CSHL-HAPMAP	HapMap-YRI	NA19094	YOR040.01	chr20-HapMap-YRI
5269	ss8337938	A/A	CSHL-HAPMAP	HapMap-YRI	NA19093	YOR040.02	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5269	ss66259129	A/G	CSHL-HAPMAP	HapMap-YRI	NA19093	YOR040.02	chr20-HapMap-YRI
5271	ss8337938	N/N	CSHL-HAPMAP	HapMap-YRI	NA19103	YOR042.01	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5271	ss66259129	A/G	CSHL-HAPMAP	HapMap-YRI	NA19103	YOR042.01	chr20-HapMap-YRI
5273	ss8337938	N/N	CSHL-HAPMAP	HapMap-YRI	NA19101	YOR042.03	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5273	ss66259129	G/G	CSHL-HAPMAP	HapMap-YRI	NA19101	YOR042.03	chr20-HapMap-YRI
5286	ss8337938	N/N	CSHL-HAPMAP	HapMap-YRI	NA19211	YOR050.01	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5286	ss66259129	G/G	CSHL-HAPMAP	HapMap-YRI	NA19211	YOR050.01	chr20-HapMap-YRI
5287	ss8337938	A/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	r27_ch20_YRI_affymetrix:genomewidesnp_6.0	891007
5287	ss66259129	G/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	chr20-HapMap-YRI

Genotype data submitted for	1194	samples from	1179	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: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .