Reference SNP(refSNP) Cluster Report: rs2274328

Reference SNP(refSNP) Cluster Report: rs2274328

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/130
Map to Genome Build:	36.3

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

HGVS Names
NM_001215.2:c.202A>C
NP_001206.2:p.Met68Leu
NT_021937.18:g.3546811A>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44001229 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2274328 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
ss3210073	YUSUKE\|IMS-JST070157	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	09/05/01	10/10/03	100	Genomic	unknown
ss13438851	SC_SNP\|NT_028054.12_3136503	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	10/23/03	10/25/06	119	Genomic	unknown
ss15391385	SC_SNP\|NT_021937.16_3136503	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	11/14/03	11/22/03	120	Genomic	unknown
ss23154565	PERLEGEN\|afd0985577	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	08/10/04	10/26/06	123	Genomic	unknown
ss44001229	ABI\|hCV1739309	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	07/18/05	11/03/06	126	Genomic	unknown
ss48420281	APPLERA_GI\|hCV1739309	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	09/28/05	11/03/06	126	Genomic	unknown
ss66612409	ILLUMINA\|HumanHap300v1.1_rs2274328	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	11/09/06	11/09/06	127	Genomic	unknown
ss67240347	ILLUMINA\|HumanHap550v1.1_rs2274328	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	11/14/06	11/14/06	127	Genomic	unknown
ss67636979	ILLUMINA\|HumanHap650Yv1.0_rs2274328	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	11/14/06	11/14/06	127	Genomic	unknown
ss68758122	PERLEGEN\|PGP00985577	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	01/30/07	08/14/07	127	Genomic	unknown
ss70718687	ILLUMINA\|HumanHap550v3.0__rs2274328	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	04/20/07	03/30/08	130	Genomic	unknown
ss71286900	ILLUMINA\|HumanHap650Yv3.0_rs2274328	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	04/23/07	04/23/07	127	Genomic	unknown
ss75467862	ILLUMINA\|ILMN_Human_1M_rs2274328	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	08/28/07	08/29/07	129	Genomic	unknown
ss79125166	ILLUMINA\|HumanHap300v2.0_rs2274328	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	04/18/07	11/18/07	130	Genomic	unknown
ss84015996	KRIBB_YJKIM\|KHS602641	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	12/04/07	12/06/07	130	Genomic	unknown
ss107980464	1000GENOMES\|CEU.trio.12.15.2008_11332_chr1_8932031	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	12/15/08	12/15/08	130	Genomic	unknown
ss110031150	1000GENOMES\|NA19240_2008_12_16_11518_chr1_8932031	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	12/16/08	12/17/08	130	Genomic	unknown
ss118487033	ILLUMINA-UK\|NA18507_000011249_NCBI36.1_chr1_8932031	fwd/T	A/C	cggtacaacccctccttgaaggggctcaat	tgacaggctatgagacccaggcaggggagt	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 TTGGAGTTGA CCTCGTTGTC TTTTTGGCCT CCTTCTGGGG GACCTGCTTC TGCTTTCTGG
 AAGGTGCCTC CGTGGGTCCC CGCCCAGCAG GCCCTGGCCT CTGGCCTCTG GCCTGGTGAG
 GTTCCTCCAG AGTGGGCGCA GCCAGGCAGC CCCTTGAACT GTGTCTTTCC TGTCTTAGAA
 GGGGCACTGG ACGAAGCGCA CTGGCCACAG CACTACCCCG CCTGTGGGGG CCAGAGACAG
 TCGCCTATCA ACCTACAGAG GACGAAGGTG CGGTACAACC CCTCCTTGAA GGGGCTCAAT
 M
 TGACAGGCTA TGAGACCCAG GCAGGGGAGT TCCCCATGGT CAACAATGGC CACACAGGTA
 AGAGGAAGGG GTGGTGAGGG GCTCCAGTCC ATGGGCAGCC TGCAGGGGAA GGCAGGTTAC
 ACGTGTCCCT GCCAGGAATG GCTTGCACAG AGACACAGAG CACGGCCTCA GAGCTGGAGG
 CCTCGAACAT GAGGGTCGAA CATGAGGGCT GACTGGCCCC GAAACCTAGT GGCTCTTCCA
 GAGAGGGCAG CATCCATCTT TCGACTCAAC TCCCTGCTGG TCCCTTCCTG CAGCGTTATC

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_028054

dbSNP Blast Analysis

UniGene Cluster ID
100322

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C	N
ss13438851	CHMJ	Asian	74	IG					0.514	0.365	0.122

ss23154565	AFD_EUR_PANEL	European	46	IG	0.391	0.435	0.174	0.752	0.609	0.391

	AFD_AFR_PANEL	African American	44	IG	0.227	0.500	0.273	1.000	0.477	0.523

	AFD_CHN_PANEL	Asian	46	IG	0.565	0.217	0.217	0.020	0.674	0.326

ss44001229	HapMap-CEU	European	120	IG	0.300	0.517	0.183	0.752	0.558	0.442

	HapMap-HCB	Asian	90	IG	0.267	0.533	0.200	0.655	0.533	0.467

	HapMap-JPT	Asian	90	IG	0.400	0.378	0.222	0.150	0.589	0.411

	HapMap-YRI	Sub-Saharan African	120	IG	0.233	0.467	0.300	0.752	0.467	0.533

	AoD_African_American		90	AF					0.520	0.480

	AoD_Caucasian		92	AF					0.420	0.580

	AoD_Japanese		90	AF					0.690	0.310

ss48420281	AGI_ASP population	multiple	68	IG	0.324	0.324	0.353	0.050	0.485	0.515

ss68758122	HapMap-CEU	European	118	GF	0.254	0.559	0.186		0.534	0.466

	HapMap-HCB	Asian	90	GF	0.200	0.600	0.200		0.500	0.500

	HapMap-JPT	Asian	90	GF	0.356	0.489	0.156		0.600	0.400

	HapMap-YRI	Sub-Saharan African	120	GF	0.133	0.450	0.417		0.358	0.642

Concordant Genotype	Total Sample	A/A	A/C	C/C
ss23154565	70	26	26	15
ss44001229	1165	316	554	273
ss48420281	38	11	11	12

RefSNP Genotype Summary	Total Individual	A/A	A/C	C/C
rs2274328	1301	349	587	299

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
151	ss44001229	A/C	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	r27_ch1_CEU_illumina:human_1m_beadchip	207407
159	ss44001229	A/A	CSHL-HAPMAP	HapMap-CEU	NA12146	CEPH1334.12	r27_ch1_CEU_illumina:human_1m_beadchip	207407
172	ss44001229	C/C	CSHL-HAPMAP	HapMap-CEU	NA07056	CEPH1340.12	r27_ch1_CEU_illumina:human_1m_beadchip	207407
174	ss44001229	N/N	CSHL-HAPMAP	HapMap-CEU	NA07048	CEPH1341.01	r27_ch1_CEU_illumina:human_1m_beadchip	207407
175	ss44001229	C/C	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	r27_ch1_CEU_illumina:human_1m_beadchip	207407
187	ss44001229	A/C	CSHL-HAPMAP	HapMap-CEU	NA06985	CEPH1341.14	r27_ch1_CEU_illumina:human_1m_beadchip	207407
188	ss23154565	A/A	PERLEGEN	AFD_EUR_PANEL	NA10851		71_IND_CHR_1
188	ss44001229	N/N	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	r27_ch1_CEU_illumina:human_1m_beadchip	207407
225	ss44001229	A/A	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r27_ch1_CEU_illumina:human_1m_beadchip	207407
226	ss44001229	A/A	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r27_ch1_CEU_illumina:human_1m_beadchip	207407
366	ss44001229	C/C	CSHL-HAPMAP	HapMap-CEU	NA10863	CEPH1375.02	r27_ch1_CEU_illumina:human_1m_beadchip	207407
457	ss44001229	C/C	CSHL-HAPMAP	HapMap-CEU	NA10839	CEPH1420.02	r27_ch1_CEU_illumina:human_1m_beadchip	207407
578	ss44001229	A/C	CSHL-HAPMAP	HapMap-CEU	NA12814	CEPH1454.14	r27_ch1_CEU_illumina:human_1m_beadchip	207407
5144	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5150	ss44001229	A/A	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	r27_ch1_CHB_illumina:human_1m_beadchip	207407
5151	ss44001229	C/C	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	r27_ch1_CHB_illumina:human_1m_beadchip	207407
5160	ss44001229	A/A	CSHL-HAPMAP	HapMap-HCB	NA18545	CH18545	r27_ch1_CHB_illumina:human_1m_beadchip	207407
5161	ss44001229	A/C	CSHL-HAPMAP	HapMap-HCB	NA18572	CH18572	r27_ch1_CHB_illumina:human_1m_beadchip	207407
5173	ss44001229	A/A	CSHL-HAPMAP	HapMap-HCB	NA18612	CH18612	r27_ch1_CHB_illumina:human_1m_beadchip	207407
5193	ss44001229	A/A	CSHL-HAPMAP	HapMap-JPT	NA18942	JA18942	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5195	ss44001229	A/C	CSHL-HAPMAP	HapMap-JPT	NA18951	JA18951	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5199	ss44001229	C/C	CSHL-HAPMAP	HapMap-JPT	NA18945	JA18945	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5200	ss44001229	A/A	CSHL-HAPMAP	HapMap-JPT	NA18949	JA18949	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5213	ss44001229	A/A	CSHL-HAPMAP	HapMap-JPT	NA18973	JA18973	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5217	ss44001229	A/A	CSHL-HAPMAP	HapMap-JPT	NA18976	JA18976	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5224	ss44001229	C/C	CSHL-HAPMAP	HapMap-JPT	NA18974	JA18974	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5225	ss44001229	C/C	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5226	ss44001229	A/A	CSHL-HAPMAP	HapMap-JPT	NA18990	JA18990	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5230	ss44001229	A/C	CSHL-HAPMAP	HapMap-JPT	NA18997	JA18997	r27_ch1_JPT_illumina:human_1m_beadchip	207407
5237	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA18501	YOR004.03	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5256	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA18854	YOR018.01	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5262	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA18863	YOR024.01	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5263	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA18861	YOR024.02	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5264	ss44001229	A/A	CSHL-HAPMAP	HapMap-YRI	NA18862	YOR024.03	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5268	ss44001229	C/C	CSHL-HAPMAP	HapMap-YRI	NA19094	YOR040.01	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5269	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA19093	YOR040.02	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5275	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5277	ss44001229	A/A	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5287	ss44001229	A/A	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5293	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5294	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA19160	YOR056.03	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5302	ss44001229	A/C	CSHL-HAPMAP	HapMap-YRI	NA19140	YOR071.02	r27_ch1_YRI_illumina:human_1m_beadchip	207407
5307	ss44001229	N/N	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	r27_ch1_YRI_illumina:human_1m_beadchip	207407

Genotype data submitted for	1316	samples from	1301	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

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .