Reference SNP(refSNP) Cluster Report: rs2234951

Reference SNP(refSNP) Cluster Report: rs2234951

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	98/130
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NM_000846.3:c.328C>T
NP_000837.2:p.Pro110Ser

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76893499 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2234951 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
ss869780	UWGC\|hgsta2-e5+f56	fwd/B	C/T	gcagatttgggtgaaatgatccttcttctg	cctttagtcaacctgaggaacaagatgcca	09/12/01	04/07/04	100	Genomic	unknown
ss3188821	HGBASE\|SNP000064576	fwd/B	C/T	tttgggtgaaatgatccttcttctg	cctttagtcaacctgaggaacaaga	07/23/01	10/10/03	98	cDNA	unknown
ss23948455	PERLEGEN\|afd4513913	rev/T	A/G	tggcatcttgttcctcaggttgactaaagg	cagaagaaggatcatttcacccaaatctgc	08/10/04	09/13/04	124	Genomic	unknown
ss68387861	CSHL-HAPMAP\|sanger:assay:1730648:1	rev/T	A/G	tggcatcttgttcctcaggttgactaaagg	cagaagaaggatcatttcacccaaatctgc	01/11/07	01/16/07	127	NA	unknown
ss68977271	PERLEGEN\|PGP04513913	rev/T	A/G	tggcatcttgttcctcaggttgactaaagg	cagaagaaggatcatttcacccaaatctgc	01/30/07	08/14/07	127	Genomic	unknown
ss74901090	ILLUMINA\|ILMN_Human_1M_rs2234951	fwd/B	C/T	gcagatttgggtgaaatgatccttcttctg	cctttagtcaacctgaggaacaagatgcca	08/28/07	08/29/07	129	Genomic	unknown
ss76893499	SI_EXO\|NT_007592.14_43475969	rev/T	A/G	tggcatcttgttcctcaggttgactaaagg	cagaagaaggatcatttcacccaaatctgc	09/20/07	09/20/07	129	Genomic	unknown
ss84168926	PHARMGKB_AB_DME\|PS206042_PA147532307_301	rev/T	A/G	tggcatcttgttcctcaggttgactaaagg	cagaagaaggatcatttcacccaaatctgc	12/06/07	12/09/07	130	Genomic	unknown
ss86238179	CORNELL\|hCV12027714	rev/B	C/T	tggcatcttgttcctcaggttgactaaagg	cagaagaaggatcatttcacccaaatctgc	01/21/08	01/21/08	129	Genomic	unknown
ss105440014	SNP500CANCER\|GSTA2-07	fwd/B	C/T	gcagatttgggtgaaatgatccttcttctg	cctttastcaacctgaggaacaagatgcca	09/05/08	09/05/08	130	Genomic	unknown

Fasta sequence (Legend)

 CCTGGCACAG CATCAGTGGG TACTGGCAGT GATTCCACCA ATTTCTCTCA TGACTGTGAC
 CACCGATGAT CTTCTTCCTG TATTAGGTCA TGCGTGTAAC AAAATTTAGA GAGCTATCTA
 CCTTGATAGG CTGTTTTAAG AAATAAATGT TAATATACCT GTAAAACTCA GAGCATAATG
 ACTATATACC TGTAAAACTC AGAGCATAAT GACTAGACTA TAAAAGGCAC TCATTGGAGG
 TGAATTATTT TGCCATCACC TGATACTCTA CTCTCTTAGG TTTTTATAAA CCTATAAAAT
 CTAAGGCAAA AGATATTTGA CCATTTGGTT GTTTTTGTCT TTCAGGATTG ATATGTATAT
 AGAAGGTATA GCAGATTTGG GTGAAATGAT CCTTCTTCTG
 Y
 CCTTTAGTCA ACCTGAGGAA CAAGATGCCA AGCTTGCCTT GATCCAAGAG AAAACAAAAA
 ATCGCTACTT CCCTGCCTTT GAAAAAGTAA GTGAAGCTGT TCAGTGTTTT GGGGAACTGA
 GTTTAGAAGC CAGTAGAAAA ATAGTGGCTG GGCATTCCTG GGGCACTGAT CTTCACTTTC
 AGTGATACTT CCTGGACACC AATGCAGCAC TCTGACTCTC AAGGCATTTT ATGAAAATAG
 ACTTGGAGAA ACAATTGTAT CACTTATACC CAAGCTATAA TCTTCCAGTA AAATTTTAAT
 TTACTGAACC CCAATATGGA ATTATCTGTT CAACAGAATT TTGTGTTCAT AAGTAGAATG
 TGGGCTGTGG AAGGCTCTGG ACCACACTAG AGTTGCTGTT

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
NT_007592.14

dbSNP Blast Analysis

UniGene Cluster ID
94107 446309

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss105440014	P1		204	GF	0.863	0.118	0.020		0.922	0.078

	CAUC1		62	GF	0.903	0.097			0.952	0.048

	AFR1		48	GF	1.000				1.000

	HISP1		46	GF	0.913	0.087			0.957	0.043

	PAC1		48	GF	0.625	0.292	0.083		0.771	0.229

	P2		416	GF	0.880	0.120			0.940	0.060

	CAUC2		120	GF	0.883	0.117			0.942	0.058

	AFR2		120	GF	1.000				1.000

	P3		552	GF	0.909	0.083	0.007		0.951	0.049

	CAUC3		132	GF	0.970	0.030			0.985	0.015

	AFR3		150	GF	1.000				1.000

	HISP3		94	GF	1.000				1.000

	PAC3		176	GF	0.739	0.239	0.023		0.858	0.142

	ASI2		176	GF	0.795	0.205			0.898	0.102

ss23948455	AFD_EUR_PANEL	European	48	IG	0.958	0.042		1.000	0.979	0.021

	AFD_AFR_PANEL	African American	46	IG	1.000				1.000

	AFD_CHN_PANEL	Asian	44	IG	0.864	0.136		0.752	0.932	0.068

	HapMap-CEU	European	116	IG	0.914	0.086		0.752	0.957	0.043

	HapMap-HCB	Asian	76	IG	0.921	0.079		0.403	0.961	0.039

	HapMap-JPT	Asian	72	IG	0.972	0.028		0.527	0.986	0.014

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

ss68977271	HapMap-CEU	European	120	GF	0.783	0.100	0.117		0.833	0.167

	HapMap-HCB	Asian	90	GF	0.733	0.156	0.111		0.811	0.189

	HapMap-JPT	Asian	88	GF	0.705	0.227	0.068		0.818	0.182

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

ss84168926	PA147532308		356	AF					0.947	0.053

ss869780	NIHPDR	Global	92	IG	0.957	0.043		1.000	0.978	0.022

Concordant Genotype	Total Sample	C/C	C/T
ss23948455	70
ss76893499	1181
ss869780	46	44	2

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2234951	1309	44	2

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
200	ss76893499	A/G	CSHL-HAPMAP	HapMap-CEU	NA12057	CEPH1344.13	r27_ch6_CEU_illumina:human_1m_beadchip
203	ss23948455	G/G	PERLEGEN	AFD_EUR_PANEL	NA07348		71_IND_CHR_6
203	ss76893499	G/G	CSHL-HAPMAP	HapMap-CEU	NA07348	CEPH1345.02	r27_ch6_CEU_illumina:human_1m_beadchip
213	ss76893499	A/G	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	r27_ch6_CEU_illumina:human_1m_beadchip
345	ss76893499	N/N	CSHL-HAPMAP	HapMap-CEU	NA12717	CEPH1358.12	r27_ch6_CEU_illumina:human_1m_beadchip
363	ss76893499	G/G	CSHL-HAPMAP	HapMap-CEU	NA11995	CEPH1362.16	r27_ch6_CEU_illumina:human_1m_beadchip
438	ss76893499	A/G	CSHL-HAPMAP	HapMap-CEU	NA12248	CEPH1416.11	r27_ch6_CEU_illumina:human_1m_beadchip
465	ss76893499	N/N	CSHL-HAPMAP	HapMap-CEU	NA12004	CEPH1420.10	r27_ch6_CEU_illumina:human_1m_beadchip
535	ss76893499	G/G	CSHL-HAPMAP	HapMap-CEU	NA12750	CEPH1444.13	r27_ch6_CEU_illumina:human_1m_beadchip
536	ss76893499	A/G	CSHL-HAPMAP	HapMap-CEU	NA12751	CEPH1444.14	r27_ch6_CEU_illumina:human_1m_beadchip
546	ss76893499	G/G	CSHL-HAPMAP	HapMap-CEU	NA12761	CEPH1447.10	r27_ch6_CEU_illumina:human_1m_beadchip
577	ss76893499	A/G	CSHL-HAPMAP	HapMap-CEU	NA12813	CEPH1454.13	r27_ch6_CEU_illumina:human_1m_beadchip
636	ss76893499	G/G	CSHL-HAPMAP	HapMap-CEU	NA12891	CEPH1463.15	r27_ch6_CEU_illumina:human_1m_beadchip
5156	ss76893499	A/G	CSHL-HAPMAP	HapMap-HCB	NA18603	CH18603	r27_ch6_CHB_illumina:human_1m_beadchip
5157	ss76893499	N/N	CSHL-HAPMAP	HapMap-HCB	NA18540	CH18540	r27_ch6_CHB_illumina:human_1m_beadchip
5158	ss76893499	G/G	CSHL-HAPMAP	HapMap-HCB	NA18605	CH18605	r27_ch6_CHB_illumina:human_1m_beadchip
5162	ss76893499	N/N	CSHL-HAPMAP	HapMap-HCB	NA18547	CH18547	r27_ch6_CHB_illumina:human_1m_beadchip
5167	ss76893499	G/G	CSHL-HAPMAP	HapMap-HCB	NA18611	CH18611	r27_ch6_CHB_illumina:human_1m_beadchip
5172	ss76893499	A/G	CSHL-HAPMAP	HapMap-HCB	NA18570	CH18570	r27_ch6_CHB_illumina:human_1m_beadchip
5181	ss76893499	G/G	CSHL-HAPMAP	HapMap-HCB	NA18576	CH18576	r27_ch6_CHB_illumina:human_1m_beadchip
5203	ss76893499	G/G	CSHL-HAPMAP	HapMap-JPT	NA18956	JA18956	r27_ch6_JPT_illumina:human_1m_beadchip
5209	ss76893499	G/G	CSHL-HAPMAP	HapMap-JPT	NA18960	JA18960	r27_ch6_JPT_illumina:human_1m_beadchip
5222	ss76893499	A/G	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	r27_ch6_JPT_illumina:human_1m_beadchip
5223	ss76893499	G/G	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	r27_ch6_JPT_illumina:human_1m_beadchip
5227	ss76893499	G/G	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	r27_ch6_JPT_illumina:human_1m_beadchip
5234	ss76893499	G/G	CSHL-HAPMAP	HapMap-JPT	NA18999	JA18999	r27_ch6_JPT_illumina:human_1m_beadchip
5280	ss76893499	G/G	CSHL-HAPMAP	HapMap-YRI	NA19173	YOR047.01	r27_ch6_YRI_perlegen:genotyping_1.0.0

Genotype data submitted for	1324	samples from	1309	individuals	Individual with multiple genotypes submission:	15

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .