Reference SNP(refSNP) Cluster Report: rs3740015

Reference SNP(refSNP) Cluster Report: rs3740015

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/130
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NM_018706.5:c.814T>G
NP_061176.3:p.Tyr272Asp
NT_077569.2:g.6493977T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38561575 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3740015 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
ss4926018	YUSUKE\|IMS-JST090874	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	07/29/02	10/10/03	107	Genomic	unknown
ss15892199	SC_SNP\|NT_077569.2_6493977	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	11/17/03	10/26/06	120	Genomic	unknown
ss24302960	PERLEGEN\|afd4109357	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	08/10/04	09/13/04	123	Genomic	unknown
ss28497330	MGC_GENOME_DIFF\|29800963-T6493977G	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	08/20/04	08/20/04	126	cDNA	unknown
ss28511986	MGC_GENOME_DIFF\|BC002477x29800963-T6493977G	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	08/25/04	08/25/04	126	cDNA	unknown
ss38561575	ABI\|hCV1525213	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	07/15/05	11/02/06	126	Genomic	unknown
ss48422689	APPLERA_GI\|hCV1525213	rev/T	A/C	tcacatggaggggatggtgcgccccaaagt	caggtccacagaggaggtcaggtgagacag	09/28/05	11/03/06	126	Genomic	unknown
ss66681255	ILLUMINA\|HumanHap300v1.1_rs3740015	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	11/09/06	11/09/06	127	Genomic	unknown
ss67298296	ILLUMINA\|HumanHap550v1.1_rs3740015	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	11/14/06	11/14/06	127	Genomic	unknown
ss67702870	ILLUMINA\|HumanHap650Yv1.0_rs3740015	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	11/14/06	11/14/06	127	Genomic	unknown
ss69070765	PERLEGEN\|PGP04109357	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	01/30/07	03/31/08	127	Genomic	unknown
ss70776926	ILLUMINA\|HumanHap550v3.0__rs3740015	rev/T	A/C	tcacatggaggggatggtgcgccccaaagt	caggtccacagaggaggtcaggtgagacag	04/20/07	03/30/08	130	Genomic	unknown
ss71353039	ILLUMINA\|HumanHap650Yv3.0_rs3740015	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	04/23/07	04/23/07	127	Genomic	unknown
ss74806194	AFFY\|SNP_M-174948	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	08/09/07	08/09/07	128	Genomic	unknown
ss75557393	ILLUMINA\|ILMN_Human_1M_rs3740015	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	08/28/07	08/29/07	129	Genomic	unknown
ss79163792	ILLUMINA\|HumanHap300v2.0_rs3740015	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	04/18/07	11/18/07	130	Genomic	unknown
ss84162437	KRIBB_YJKIM\|KHS648192	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	12/04/07	12/06/07	130	Genomic	unknown
ss88098962	BCMHGSC_JDW\|JWB-0236804	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	02/26/08	02/27/08	129	Genomic	unknown
ss97536202	HUMANGENOME_JCVI\|1103649863819	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	03/29/08	03/29/08	130	Genomic	unknown
ss109238994	1000GENOMES\|CEU.trio.12.15.2008_2296939_chr10_12171087	fwd/B	G/T	ctgtctcacctgacctcctctgtggacctg	actttggggcgcaccatcccctccatgtga	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 ACCATGTTGG CCAGGCTGGT CCCGAACTCC TGACCTCAAG TGATCTTCCC GTCTCAGCCT
 CCCAAAGTGC TGGAATTACA GGCATAAGCC ACCACTCCTG GCTTTAAATT TTCTTTTTTG
 TTGTATGATT TCAACTCAGC ACTTCTTCCC TAGACTCCAT TGTGATGAAT GCCATTTTTT
 TCCTTTTGAA TGTATCCACA ATAGCTGATG TTCCGTAAAA TGCGAGGCTT AAGTGAATTT
 CCAGAGAATT TCTCAGCCAC TGGAGACGTC CTGTCTCACC TGACCTCCTC TGTGGACCTG
 K
 ACTTTGGGGC GCACCATCCC CTCCATGTGA CAATGTTGCC CAATCCCTCG CACCTGGAGG
 CCGTCAACCC CGTGGCCGTG GGCAAAACTC GCGGCAGGCA GCAGTCTCGC CAAGACGGCG
 ATTACTCTCC AGACAACTCA GCCCAGCCGG GGGACAGGGT CATTTGCTTA CAGGTACTTG
 GAGCTTCTGA AATTGAGGCC AGAGGTGGGG AAAACTGGGA AGAATGTGTG GGTTGGGAGG
 GCTGAAAGCA CATGGCAGAC ATTCATGATG AAACTGAGAT GACCTTTTGG AAAAAGATTC

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_077569 ABBA01034673 BC002477

dbSNP Blast Analysis

UniGene Cluster ID
104980

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss15892199	CHMJ	Asian	74	IG					0.446	0.554

ss24302960	AFD_EUR_PANEL	European	46	IG	0.174	0.652	0.174	0.150	0.500	0.500

	AFD_AFR_PANEL	African American	40	IG	0.050	0.550	0.400	0.273	0.325	0.675

	AFD_CHN_PANEL	Asian	48	IG	0.333	0.500	0.167	1.000	0.583	0.417

ss38561575	HapMap-CEU	European	120	IG	0.367	0.550	0.083	0.150	0.642	0.358

	HapMap-HCB	Asian	88	IG	0.273	0.523	0.205	0.655	0.534	0.466

	HapMap-JPT	Asian	86	IG	0.326	0.512	0.163	1.000	0.581	0.419

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.200	0.783	1.000	0.117	0.883

	AoD_African_American		90	AF					0.330	0.670

	AoD_Caucasian		92	AF					0.660	0.340

	AoD_Chinese		90	AF					0.400	0.600

	AoD_Japanese		90	AF					0.510	0.490

ss48422689	AGI_ASP population	multiple	74	IG	0.216	0.541	0.243	0.655	0.486	0.514

ss4926018	JBIC-allele		1112	AF					0.535	0.465

ss69070765	HapMap-CEU	European	120	GF	0.367	0.550	0.083		0.642	0.358

	HapMap-HCB	Asian	90	GF	0.267	0.533	0.200		0.533	0.467

	HapMap-JPT	Asian	90	GF	0.311	0.511	0.178		0.567	0.433

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.183	0.800		0.108	0.892

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss24302960	71	13	38	16
ss38561575	1202	259	504	416
ss48422689	37
ss69070765	265	56	110	99
ss97536202	1	1

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs3740015	1301	277	544	434

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5149	ss38561575	G/T	CSHL-HAPMAP	HapMap-HCB	NA18524	CH18524	r27_ch10_CHB_illumina:human_1m_beadchip	780767
5149	ss69070765	G/T	CSHL-HAPMAP	HapMap-HCB	NA18524	CH18524	chr10-HapMap-HCB
5151	ss38561575	G/T	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	r27_ch10_CHB_illumina:human_1m_beadchip	780767
5151	ss69070765	G/T	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	chr10-HapMap-HCB
5164	ss38561575	G/G	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	r27_ch10_CHB_illumina:human_1m_beadchip	780767
5164	ss69070765	G/G	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	chr10-HapMap-HCB
5169	ss38561575	G/G	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	r27_ch10_CHB_illumina:human_1m_beadchip	780767
5169	ss69070765	G/G	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	chr10-HapMap-HCB
5261	ss38561575	N/N	CSHL-HAPMAP	HapMap-YRI	NA18856	YOR023.03	r27_ch10_YRI_illumina:human_1m_beadchip	780767
5261	ss69070765	T/T	CSHL-HAPMAP	HapMap-YRI	NA18856	YOR023.03	chr10-HapMap-YRI

Genotype data submitted for	1316	samples from	1301	individuals	Individual with multiple genotypes submission:	276

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .