Reference SNP(refSNP) Cluster Report: rs1046404

Reference SNP(refSNP) Cluster Report: rs1046404

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/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_052935.3:c.614C>G
NP_443167.3:p.Ser205Cys
NT_010755.15:g.3708104G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44005962 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1046404 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
ss1517550	LEE\|224385	fwd/T	C/G	acaacaagaacagctctgtgtgtgagaact	tggttacttccagcaacttgagggcaaaac	09/13/00	10/10/03	86	cDNA	unknown
ss4409950	LEE\|e224385	fwd/T	C/G	acaacaagaacagctctgtgtgtgagaact	tggttacttccagcaacttgagggcaaaac	04/26/02	10/10/03	106	cDNA	unknown
ss14282709	BCM_SSAHASNP\|chr17.NT_010755.14_3706306	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	11/05/03	10/25/06	119	Genomic	unknown
ss16733255	CSHL-HAPMAP\|CSHL-HuAA-200402.chr17.NT_010755.14_3706306	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	02/17/04	03/04/04	120	Genomic	unknown
ss19357433	CSHL-HAPMAP\|CSHL-HuDD-200402.chr17.NT_010755.14_3706306	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	02/20/04	03/04/04	120	Genomic	unknown
ss20032182	CSHL-HAPMAP\|CSHL-HuFF-200402.chr17.NT_010755.14_3706306	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	02/21/04	03/04/04	120	Genomic	unknown
ss21397023	SSAHASNP\|WGSA-200403-chr17.chr17.NT_010755.14_3706306	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	03/19/04	03/20/04	121	Genomic	unknown
ss24563126	PERLEGEN\|afd2484767	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	08/10/04	09/13/04	123	Genomic	unknown
ss24815629	SEQUENOM\|sqnm210263	fwd/T	C/G	acaacaagaacagctctgtgtgtgagaact	tggttacttccagcaacttgagggcaaaac	06/18/04	08/05/04	123	cDNA	unknown
ss28497779	MGC_GENOME_DIFF\|37543812-G3706306C	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	08/20/04	08/20/04	126	cDNA	unknown
ss28512553	MGC_GENOME_DIFF\|BC013742x37543812-G3706306C	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	08/25/04	08/25/04	126	cDNA	unknown
ss28512575	MGC_GENOME_DIFF\|BC014132x37543812-G3706306C	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	08/25/04	08/25/04	126	cDNA	unknown
ss28512718	MGC_GENOME_DIFF\|BC016971x37543812-G3706306C	rev/B	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	08/25/04	08/25/04	126	cDNA	unknown
ss44005962	ABI\|hCV9256714	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacacagagctgttcttgttgt	07/18/05	11/03/06	126	Genomic	unknown
ss48417778	APPLERA_GI\|hCV9256714	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacacagagctgttcttgttgt	09/28/05	11/03/06	126	Genomic	unknown
ss65724666	ILLUMINA\|Human1-rs1046404	fwd/T	C/G	acaacaagaacagctctgcgtgtgagaact	tggttacttccagcaacttgagggcaaaac	10/10/06	10/10/06	127	Genomic	unknown
ss69196383	PERLEGEN\|PGP02484767	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	01/30/07	08/14/07	127	Genomic	unknown
ss74812690	AFFY\|SNP_M-288596	fwd/T	C/G	acaacaagaacagctctgcgtgtgagaact	tggttacttccagcaacttgagggcaaaac	08/09/07	08/09/07	128	Genomic	unknown
ss74855553	ILLUMINA\|ILMN_Human_1M_rs1046404	fwd/	C/G	acaacaagaacagctctgtgtgtgagaact	tggttacttccagcaacttgagggcaaaac	08/28/07	08/29/07	129	Genomic	unknown
ss77746399	HGSV\|Cor12156_SNV_20070510.chr17_37237334	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	10/09/07	10/14/07	129	Genomic	unknown
ss78680565	HGSV\|Cor12878_SNV_20070510.chr17_37237334	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	10/17/07	10/20/07	129	Genomic	unknown
ss90588852	BCMHGSC_JDW\|JWB-1021706	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	02/26/08	02/29/08	129	Genomic	unknown
ss96594224	HUMANGENOME_JCVI\|1103645325311	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacacagagctgttcttgttgt	03/26/08	03/26/08	130	Genomic	unknown
ss109765360	1000GENOMES\|CEU.trio.12.15.2008_3399073_chr17_37237334	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	12/15/08	12/16/08	130	Genomic	unknown
ss113535824	1000GENOMES\|NA19240_2008_12_16_3058247_chr17_37237334	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	12/18/08	12/18/08	130	Genomic	unknown
ss118055100	ILLUMINA-UK\|NA18507_000043637_NCBI36.1_chr17_37237334	rev/	C/G	gttttgccctcaagttgctggaagtaacca	agttctcacacgcagagctgttcttgttgt	01/20/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 AAGCAGCCAT AGGCATCATG TAAACAAATG AGTTTGGCTG TATCCCAATA CAACTTTATT
 TACAAAAGCA GGCCAAGTCT GGCCCATGGG CCGTAGTTTA GGCTACAGTG AAGTTTTGGC
 ATTATCTATC ACTTTTGGGA TTCCCTTTTC TCTGTGACAG AGACAGTGGA GAGCTGGTGC
 CACATGGGTC CCTGCAGCCC TTCCATCTGT CTCTTGTCTT CATTATTTAG GGTTTTCTCC
 AGGGATTTAA GGGCCAGCTC ATACACACAT ACAACAAGAA CAGCTCTGTG TGTGAGAACT
 S
 TGGTTACTTC CAGCAACTTG AGGGCAAAAC CAATGTCATC CTGCTGGGAG ACTCTATCGG
 GGACCTCACC ATGGCCGATG GGGTTCCTGG TGTGCAGAAC ATTCTCAAAA TTGGCTTCCT
 GAATGACAAG GTGGGTAGAG GACCAGGGCT GCTTCTCTTC ATGGCTTTCT TCTCTTTGAA
 TGCCCATTAA CAAATGCCTT TGAACACATT CTCTTTTTTT ATTTCTATTT TTATTTTATT
 TTATTTTATT TTTTTTTGAG ACGGGGTCTC ACTCTGTCGC CCAGGCTGGA GTGCAGTGGC

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
dbSTS	GenBank
sqnm210263	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/G	G/G	HWP	C	G
ss14282709	CHMJ	Asian	74	IG					0.135	0.865

ss24563126	AFD_EUR_PANEL	European	48	IG		0.458	0.542	0.150	0.229	0.771

	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

ss24815629	CEPH		184	AF					0.190	0.810

ss44005962	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	120	IG	0.050	0.300	0.650	0.655	0.200	0.800

ss48417778	AGI_ASP population	multiple	76	IG	0.053	0.526	0.421	0.200	0.316	0.684

ss69196383	HapMap-CEU	European	120	GF	0.050	0.383	0.567		0.242	0.758

	HapMap-HCB	Asian	90	GF	0.022	0.422	0.556		0.233	0.767

	HapMap-JPT	Asian	90	GF		0.267	0.733		0.133	0.867

	HapMap-YRI	Sub-Saharan African	120	GF	0.050	0.300	0.650		0.200	0.800

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.333+/-0.236	620	497	276	0

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 .