Reference SNP(refSNP) Cluster Report: rs1046403

Reference SNP(refSNP) Cluster Report: rs1046403

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/130
Map to Genome Build:	36.3

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

HGVS Names
NM_052935.3:c.602C>T
NP_443167.3:p.Ala201Val
NT_010755.15:g.3708116G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14282715 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1046403 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
ss1517549	LEE\|224371	fwd/B	C/T	tgatacacacatacaacaagaacagctctg	gtgtgagaactgtggttacttccagcaact	09/13/00	10/10/03	86	cDNA	unknown
ss4409949	LEE\|e224371	fwd/B	C/T	tgatacacacatacaacaagaacagctctg	gtgtgagaactgtggttacttccagcaact	04/26/02	10/10/03	106	cDNA	unknown
ss14282715	BCM_SSAHASNP\|chr17.NT_010755.14_3706318	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	11/05/03	10/25/06	119	Genomic	unknown
ss16733261	CSHL-HAPMAP\|CSHL-HuAA-200402.chr17.NT_010755.14_3706318	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	02/17/04	03/04/04	120	Genomic	unknown
ss19357437	CSHL-HAPMAP\|CSHL-HuDD-200402.chr17.NT_010755.14_3706318	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	02/20/04	03/04/04	120	Genomic	unknown
ss20032185	CSHL-HAPMAP\|CSHL-HuFF-200402.chr17.NT_010755.14_3706318	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	02/21/04	03/04/04	120	Genomic	unknown
ss21397058	SSAHASNP\|WGSA-200403-chr17.chr17.NT_010755.14_3706318	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	03/19/04	03/20/04	121	Genomic	unknown
ss24563136	PERLEGEN\|afd2484768	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	08/10/04	09/13/04	123	Genomic	unknown
ss28497778	MGC_GENOME_DIFF\|37543812-G3706318A	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	08/20/04	08/20/04	126	cDNA	unknown
ss28512552	MGC_GENOME_DIFF\|BC013742x37543812-G3706318A	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	08/25/04	08/25/04	126	cDNA	unknown
ss28512574	MGC_GENOME_DIFF\|BC014132x37543812-G3706318A	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	08/25/04	08/25/04	126	cDNA	unknown
ss28512717	MGC_GENOME_DIFF\|BC016971x37543812-G3706318A	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	08/25/04	08/25/04	126	cDNA	unknown
ss44036329	ABI\|hCV9256713	rev/T	A/G	agttgctggaagtaaccacagttctcacac	cagagctgttcttgttgtatgtgtgtatga	07/18/05	07/18/05	126	Genomic	unknown
ss48417779	APPLERA_GI\|hCV9256713	rev/T	A/G	agttgctggaagtaaccacagttctcacac	cagagctgttcttgttgtatgtgtgtatga	09/28/05	11/03/06	126	Genomic	unknown
ss66665294	ILLUMINA\|HumanHap300v1.1_rs1046403	fwd/B	C/T	tcatacacacatacaacaagaacagctctg	gtgtgagaactctggttacttccagcaact	11/09/06	11/09/06	127	Genomic	unknown
ss66884139	ILLUMINA\|HumanHap550v1.1_rs1046403	fwd/B	C/T	tcatacacacatacaacaagaacagctctg	gtgtgagaactctggttacttccagcaact	11/14/06	11/14/06	127	Genomic	unknown
ss66979498	ILLUMINA\|HumanHap650Yv1.0_rs1046403	fwd/B	C/T	tcatacacacatacaacaagaacagctctg	gtgtgagaactctggttacttccagcaact	11/14/06	11/14/06	127	Genomic	unknown
ss69196384	PERLEGEN\|PGP02484768	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	01/30/07	08/14/07	127	Genomic	unknown
ss70366195	ILLUMINA\|HumanHap300v2.0_rs1046403	fwd/B	C/T	tcatacacacatacaacaagaacagctctg	gtgtgagaactctggttacttccagcaact	04/18/07	11/17/07	127	Genomic	unknown
ss70479893	ILLUMINA\|HumanHap550v3.0__rs1046403	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	04/20/07	03/30/08	130	Genomic	unknown
ss71003430	ILLUMINA\|HumanHap650Yv3.0_rs1046403	fwd/B	C/T	tcatacacacatacaacaagaacagctctg	gtgtgagaactctggttacttccagcaact	04/23/07	04/23/07	127	Genomic	unknown
ss74813497	AFFY\|SNP_M-290026	fwd/B	C/T	tcatacacacatacaacaagaacagctctg	gtgtgagaactctggttacttccagcaact	08/09/07	08/09/07	128	Genomic	unknown
ss75594673	ILLUMINA\|ILMN_Human_1M_rs1046403	fwd/B	C/T	tcatacacacatacaacaagaacagctctg	gtgtgagaactctggttacttccagcaact	08/28/07	08/29/07	129	Genomic	unknown
ss77573928	HGSV\|Cor12156_SNV_20070510.chr17_37237346	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	10/09/07	10/13/07	129	Genomic	unknown
ss78425251	HGSV\|Cor12878_SNV_20070510.chr17_37237346	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	10/17/07	10/19/07	129	Genomic	unknown
ss83673066	KRIBB_YJKIM\|KHS516039	fwd/B	C/T	tcatacacacatacaacaagaacagctctg	gtgtgagaactctggttacttccagcaact	12/04/07	12/05/07	130	Genomic	unknown
ss90588854	BCMHGSC_JDW\|JWB-1021707	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	02/26/08	02/29/08	129	Genomic	unknown
ss96594225	HUMANGENOME_JCVI\|1103645325312	rev/T	A/G	agttgctggaagtaaccacagttctcacac	cagagctgttcttgttgtatgtgtgtatga	03/26/08	03/26/08	130	Genomic	unknown
ss109765364	1000GENOMES\|CEU.trio.12.15.2008_3399074_chr17_37237346	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	12/15/08	12/16/08	130	Genomic	unknown
ss113535838	1000GENOMES\|NA19240_2008_12_16_3058248_chr17_37237346	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	12/18/08	12/18/08	130	Genomic	unknown
ss118055102	ILLUMINA-UK\|NA18507_000043638_NCBI36.1_chr17_37237346	rev/T	A/G	agttgctggaagtaaccagagttctcacac	cagagctgttcttgttgtatgtgtgtatga	01/20/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 TCATTTAAAC Taggagttac aaacttatgc tgtaaaaggc cctgtcgtcg atatttaggc
 tttatgggct gtggcatcac tgttgcaact gcccaacttt gcctttatag cacaaaaaag
 cagccatagg catcatgtaa acaaatgagt ttggctgtat cccaatacaa ctttatttac
 aaaagcaggc caagtctggc ccatgggccg tagtttAGGC TACAGTGAAG TTTTGGCATT
 ATCTATCACT TTTGGGATTC CCTTTTCTCT GTGACAGAGA CAGTGGAGAG CTGGTGCCAC
 ATGGGTCCCT GCAGCCCTTC CATCTGTCTC TTGTCTTCAT TATTTAGGGT TTTCTCCAGG
 GATTTAAGGG CCAGCTCATA CACACATACA ACAAGAACAG CTCTG
 Y
 GTGTGAGAAC TCTGGTTACT TCCAGCAACT TGAGGGCAAA ACCAATGTCA TCCTGCTGGG
 AGACTCTATC GGGGACCTCA CCATGGCCGA TGGGGTTCCT GGTGTGCAGA ACATTCTCAA
 AATTGGCTTC CTGAATGACA AGGTGGGTAG AGGACCAGGG CTGCTTCTCT TCATGTCTTT
 CTTCTCTTTG AATGCCCATT

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_010755 ABBA01006449 BC013742 BC014132 BC016971 Hs.237536

dbSNP Blast Analysis

UniGene Cluster ID
237536

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss14282715	HapMap-CEU	European	120	IG	0.050	0.383	0.567	0.752	0.242	0.758

	HapMap-HCB	Asian	90	IG	0.022	0.422	0.556	0.251	0.233	0.767

	HapMap-JPT	Asian	90	IG		0.267	0.733	0.317	0.133	0.867

	HapMap-YRI	Sub-Saharan African	118	IG	0.051	0.288	0.661	0.584	0.195	0.805

	CHMJ	Asian	74	IG					0.135	0.865

ss24563136	AFD_EUR_PANEL	European	44	IG		0.409	0.591	0.251	0.205	0.795

	AFD_AFR_PANEL	African American	46	IG	0.043	0.261	0.696	0.752	0.174	0.826

	AFD_CHN_PANEL	Asian	46	IG		0.348	0.652	0.317	0.174	0.826

ss48417779	AGI_ASP population	multiple	70	IG	0.114	0.429	0.457	1.000	0.329	0.671

ss69196384	HapMap-CEU	European	120	GF	0.017	0.417	0.567		0.225	0.775

	HapMap-HCB	Asian	90	GF		0.444	0.556		0.222	0.778

	HapMap-JPT	Asian	90	GF		0.267	0.733		0.133	0.867

	HapMap-YRI	Sub-Saharan African	120	GF	0.033	0.317	0.650		0.192	0.808

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss14282715	1202
ss24563136	71
ss48417779	38
ss69196384	265
ss96594225	1

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs1046403	1302

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
213	ss14282715	G/G	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	r27_ch17_CEU_illumina:human_1m_beadchip	5401040
213	ss69196384	A/G	CSHL-HAPMAP	HapMap-CEU	NA07357	CEPH1345.12	chr17-HapMap-CEU
374	ss14282715	G/G	CSHL-HAPMAP	HapMap-CEU	NA12234	CEPH1375.12	r27_ch17_CEU_illumina:human_1m_beadchip	5401040
374	ss69196384	A/G	CSHL-HAPMAP	HapMap-CEU	NA12234	CEPH1375.12	chr17-HapMap-CEU
5139	ss14282715	N/N	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r27_ch17_YRI_illumina:human_1m_beadchip	5401040
5139	ss69196384	A/G	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	chr17-HapMap-YRI
5165	ss14282715	G/G	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	r27_ch17_CHB_illumina:human_1m_beadchip	5401040
5165	ss69196384	A/G	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	chr17-HapMap-HCB
5296	ss14282715	G/G	CSHL-HAPMAP	HapMap-YRI	NA19222	YOR058.02	r27_ch17_YRI_illumina:human_1m_beadchip	5401040
5296	ss69196384	A/G	CSHL-HAPMAP	HapMap-YRI	NA19222	YOR058.02	chr17-HapMap-YRI

Genotype data submitted for	1317	samples from	1302	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 .