Reference SNP(refSNP) Cluster Report: rs12900702

Reference SNP(refSNP) Cluster Report: rs12900702

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	121/130
Map to Genome Build:	36.3

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

HGVS Names
NM_016013.2:c.941C>G
NP_057097.2:p.Ala314Gly
NT_010194.16:g.12470242G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss21238302 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12900702 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
ss21238302	SSAHASNP\|WGSA-200403-chr15.chr15.NT_010194.16_12470242	fwd/B	C/G	cttgggttaagctctggagaattttcatag	caaattcttctgtatgagctggatcagtaa	03/19/04	03/31/08	121	Genomic	unknown
ss40634049	ABI\|hCV1117617	fwd/	C/G	cttgggttaagctctggagaattttcatag	caaattcttctgtatgagctggatcagtaa	07/17/05	07/17/05	126	Genomic	unknown
ss69174603	PERLEGEN\|PGP06400923	fwd/	C/G	cttgggttaagctctggagaattttcatag	caaattcttctgtatgagctggatcagtaa	01/30/07	03/31/08	127	Genomic	unknown
ss74820442	AFFY\|SNP_M-322978	fwd/B	C/G	cttgggttaagctctggagaattttcatag	caaattcttctgtatgagctggatcagtaa	08/09/07	08/09/07	128	Genomic	unknown
ss90135318	BCMHGSC_JDW\|JWB-0847066	fwd/	C/G	cttgggttaagctctggagaattttcatag	caaattcttctgtatgagctggatcagtaa	02/26/08	02/29/08	129	Genomic	unknown
ss96806513	HUMANGENOME_JCVI\|1103645594601	fwd/	C/G	cttgggttaagctctggagaattttcatag	caaattcttctgtatgagctggatcagtaa	03/27/08	03/27/08	130	Genomic	unknown
ss108764719	1000GENOMES\|CEU.trio.12.15.2008_3151453_chr15_39466977	fwd/	C/G	cttgggttaagctctggagaattttcatag	caaattcttctgtatgagctggatcagtaa	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 ATTATAACTT GTCTTAGAGA ATACATACTA GCCagccagg cgcggtggct cacatctgta
 atcccagcac tttgggaggc caaggcgggc ggatcacctg aggtcaggag ttcgagacca
 gcctgaccaa catggagaaa ccctgtctct actaaaaata caaaattagc tgggcatgat
 ggtgcatgcc tataatccca gctactcggg aagctgaggc aggagaatag cttgaaccca
 gaaggcgaag gttacggtga gccgagatca cgctactgca cgccagcatg ccagcctggg
 cgacagagca gaactccatc tcaaaaaaaa aaaaaaaaaa gagagagaaT ACATACTAGC
 CATTGGTTGG ATGCCATTAA AGAAATATTT TATTTTGTCT ATATCATTGT AGATGCTAGT
 ACCCTTAGAT TAGTAAAACA AAACTACCAT ATGATCTTTA TTTAAAAAGC CTTGGGTTAA
 GCTCTGGAGA ATTTTCATAG
 S
 CAAATTCTTC TGTATGAGCT GGATCAGTAA ACACGCCAAT AAAATCTATC TCCAGGAAGA
 ATGGACCATC CACTTTATCA GCCAAGGTGA ATCCTATAGA AGAGATCTAA ATTTAAAATA
 CAGAAATTGA TTAAAATCTC ATACAGTGAC GTACTGAGAT TATTCCAGGA GTTTAAAATC
 CCATCAGGTG ATGATTATAA

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_010194 ABBA01162165

dbSNP Blast Analysis

UniGene Cluster ID
106529

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss21238302	HapMap-CEU	European	116	IG	0.034	0.345	0.621		0.207	0.793

	HapMap-HCB	Asian	88	IG			1.000			1.000

	HapMap-JPT	Asian	86	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	116	IG		0.017	0.983		0.009	0.991

ss69174603	HapMap-CEU	European	120	GF		0.483	0.517		0.242	0.758

	HapMap-HCB	Asian	88	GF		0.205	0.795		0.102	0.898

	HapMap-JPT	Asian	90	GF		0.267	0.733		0.133	0.867

	HapMap-YRI	Sub-Saharan African	120	GF		0.150	0.850		0.075	0.925

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss21238302	478	1	29	185
ss96806513	1		1

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs12900702	526	1	30	185

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
169	ss21238302	C/C	CSHL-HAPMAP	HapMap-CEU	NA06994	CEPH1340.09	r27_ch15_CEU_bcm:genotype_0002
170	ss21238302	C/C	CSHL-HAPMAP	HapMap-CEU	NA07000	CEPH1340.10	r27_ch15_CEU_bcm:genotype_0002
175	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	r27_ch15_CEU_bcm:genotype_0002
188	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA10851	CEPH1344.01	r27_ch15_CEU_bcm:genotype_0002
213	ss21238302	C/G	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	r27_ch15_CEU_bcm:genotype_0002
214	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA07345	CEPH1345.13	r27_ch15_CEU_bcm:genotype_0002
229	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r27_ch15_CEU_bcm:genotype_0002
239	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA11882	CEPH1347.15	r27_ch15_CEU_bcm:genotype_0002
242	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	r27_ch15_CEU_bcm:genotype_0002
264	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA11831	CEPH1350.12	r27_ch15_CEU_bcm:genotype_0002
410	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA12155	CEPH1408.12	r27_ch15_CEU_bcm:genotype_0002
439	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	r27_ch15_CEU_bcm:genotype_0002
536	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA12751	CEPH1444.14	r27_ch15_CEU_bcm:genotype_0002
537	ss21238302	G/G	CSHL-HAPMAP	HapMap-CEU	NA12752	CEPH1447.01	r27_ch15_CEU_bcm:genotype_0002
566	ss21238302	C/C	CSHL-HAPMAP	HapMap-CEU	NA12802	CEPH1454.02	r27_ch15_CEU_bcm:genotype_0002
5135	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA19128	YOR077.03	r27_ch15_YRI_bcm:genotype_0002
5137	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	r27_ch15_YRI_bcm:genotype_0002
5138	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA19130	YOR101.03	r27_ch15_YRI_bcm:genotype_0002
5148	ss21238302	G/G	CSHL-HAPMAP	HapMap-HCB	NA18526	CH18526	r27_ch15_CHB_bcm:genotype_0002
5150	ss21238302	G/G	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	r27_ch15_CHB_bcm:genotype_0002
5155	ss21238302	G/G	CSHL-HAPMAP	HapMap-HCB	NA18537	CH18537	r27_ch15_CHB_bcm:genotype_0002
5165	ss21238302	G/G	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	r27_ch15_CHB_bcm:genotype_0002
5170	ss21238302	G/G	CSHL-HAPMAP	HapMap-HCB	NA18566	CH18566	r27_ch15_CHB_bcm:genotype_0002
5173	ss21238302	G/G	CSHL-HAPMAP	HapMap-HCB	NA18612	CH18612	r27_ch15_CHB_bcm:genotype_0002
5177	ss21238302	G/G	CSHL-HAPMAP	HapMap-HCB	NA18594	CH18594	r27_ch15_CHB_bcm:genotype_0002
5185	ss21238302	G/G	CSHL-HAPMAP	HapMap-HCB	NA18632	CH18632	r27_ch15_CHB_bcm:genotype_0002
5191	ss21238302	G/G	CSHL-HAPMAP	HapMap-HCB	NA18593	CH18593	r27_ch15_CHB_bcm:genotype_0002
5195	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18951	JA18951	r27_ch15_JPT_bcm:genotype_0002
5204	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18964	JA18964	r27_ch15_JPT_bcm:genotype_0002
5205	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18953	JA18953	r27_ch15_JPT_bcm:genotype_0002
5206	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18968	JA18968	r27_ch15_JPT_bcm:genotype_0002
5216	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18967	JA18967	r27_ch15_JPT_bcm:genotype_0002
5217	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18976	JA18976	r27_ch15_JPT_bcm:genotype_0002
5222	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18981	JA18981	r27_ch15_JPT_bcm:genotype_0002
5223	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18971	JA18971	r27_ch15_JPT_bcm:genotype_0002
5225	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	r27_ch15_JPT_bcm:genotype_0002
5228	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA18994	JA18994	r27_ch15_JPT_bcm:genotype_0002
5235	ss21238302	G/G	CSHL-HAPMAP	HapMap-JPT	NA19007	JA19007	r27_ch15_JPT_bcm:genotype_0002
5240	ss21238302	C/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	r27_ch15_YRI_bcm:genotype_0002
5257	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA18852	YOR018.02	r27_ch15_YRI_bcm:genotype_0002
5263	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA18861	YOR024.02	r27_ch15_YRI_bcm:genotype_0002
5267	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	r27_ch15_YRI_bcm:genotype_0002
5268	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA19094	YOR040.01	r27_ch15_YRI_bcm:genotype_0002
5277	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA19202	YOR045.01	r27_ch15_YRI_bcm:genotype_0002
5284	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA19204	YOR048.02	r27_ch15_YRI_bcm:genotype_0002
5296	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA19222	YOR058.02	r27_ch15_YRI_bcm:genotype_0002
5299	ss21238302	G/G	CSHL-HAPMAP	HapMap-YRI	NA19116	YOR060.02	r27_ch15_YRI_bcm:genotype_0002

Genotype data submitted for	526	samples from	526	individuals	Individual with multiple genotypes submission:	0

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 .