Reference SNP(refSNP) Cluster Report: rs8455

Reference SNP(refSNP) Cluster Report: rs8455

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/130
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NG_008441.1:g.31464T>C
NM_020169.3:c.158A>G
NM_024996.5:c.1601+4605C>T
NP_064554.3:p.His53Arg

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14195380 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs8455 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
ss10444	CGAP-GAI\|51910	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	08/23/99	10/10/03	52	cDNA	99 %
ss1530628	LEE\|538308	rev/T	A/G	aggatattccaggaagaggacataagtatc	ccttaaatttgctgttgaagaaattataca	09/13/00	10/10/03	102	cDNA	unknown
ss4420021	LEE\|e538308	rev/T	A/G	aggatattccaggaagaggacataagtatc	ccttaaatttgctgttgaagaaattataca	04/26/02	10/10/03	108	cDNA	unknown
ss10060065	BCM_SSAHASNP\|chr3.NT_005612.13_64788320	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	06/27/03	10/10/03	123	Genomic	unknown
ss14195380	BCM_SSAHASNP\|chr3.NT_005612.14_64883938	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	11/05/03	05/16/04	123	Genomic	unknown
ss16248828	CGAP-GAI\|1496145	rev/T	A/G	aggatattccaggaagaggacataagtatc	ccttaaatttgctgttgaagaaattataca	11/18/03	11/22/03	126	cDNA	unknown
ss20161954	CSHL-HAPMAP\|CSHL-HuFF-200402.chr3.NT_005612.14_64883938	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	02/21/04	03/04/04	123	Genomic	unknown
ss24381862	PERLEGEN\|afd3142912	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	08/10/04	09/13/04	123	Genomic	unknown
ss24780296	SEQUENOM\|sqnm5935	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	06/18/04	06/18/04	130	cDNA	unknown
ss24790091	SEQUENOM\|sqnm94233	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	06/18/04	06/18/04	130	cDNA	unknown
ss28510448	MGC_GENOME_DIFF\|BC005346x37550867-T64883938C	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	08/25/04	08/25/04	126	cDNA	unknown
ss48411522	APPLERA_GI\|hCV11238304	rev/T	A/G	aggatattccaggaagaggacataagtatc	ccttaaatttgctgttgaagaaattataca	09/28/05	11/03/06	126	Genomic	unknown
ss65729037	ILLUMINA\|Human1-rs8455	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	10/10/06	10/10/06	127	Genomic	unknown
ss66404026	AFFY\|SNP_A-2099103	rev/T	A/G	agaggacataagtatc	ccttaaatttgctgtt	10/29/06	08/14/07	127	Genomic	unknown
ss66661437	ILLUMINA\|HumanHap300v1.1_rs8455	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	11/09/06	11/09/06	127	Genomic	unknown
ss67879686	ILLUMINA\|HumanHap550v1.1_rs8455	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	11/14/06	11/14/06	127	Genomic	unknown
ss68021272	ILLUMINA\|HumanHap650Yv1.0_rs8455	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	11/14/06	11/15/06	127	Genomic	unknown
ss68880540	PERLEGEN\|PGP03142912	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	01/30/07	08/14/07	127	Genomic	unknown
ss70974476	ILLUMINA\|HumanHap550v3.0__rs8455	rev/T	A/G	aggatattccaggaagaggacataagtatc	ccttaaatttgctgttgaagaaattataca	04/20/07	03/31/08	130	Genomic	unknown
ss71585902	ILLUMINA\|HumanHap650Yv3.0_rs8455	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	04/23/07	04/23/07	127	Genomic	unknown
ss74811211	AFFY\|SNP_M-185135	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	08/09/07	08/09/07	128	Genomic	unknown
ss75510661	ILLUMINA\|ILMN_Human_1M_rs8455	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	08/28/07	08/29/07	129	Genomic	unknown
ss76155823	AFFY\|AFFY_6_1M_SNP_A-2099103	rev/T	A/G	agaggacataagtatc	ccttaaatttgctgtt	08/28/07	08/30/07	129	Genomic	unknown
ss77516819	HGSV\|Cor12156_SNV_20070510.chr3_159871482	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	10/09/07	10/13/07	129	Genomic	unknown
ss79283892	ILLUMINA\|HumanHap300v2.0_rs8455	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	04/18/07	11/18/07	130	Genomic	unknown
ss83348497	KRIBB_YJKIM\|KHS440393	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	12/04/07	12/04/07	130	Genomic	unknown
ss92343389	BCMHGSC_JDW\|JWB-1689029	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	02/26/08	03/02/08	129	Genomic	unknown
ss111213941	1000GENOMES\|NA19240_2008_12_16_755934_chr3_159871474	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	12/16/08	12/17/08	130	Genomic	unknown
ss112619083	1000GENOMES\|CEU.trio.12.15.2008_842766_chr3_159871474	fwd/B	C/T	tgtataatttcttcaacagcaaatttaagg	gatacttatgtcctcttcctggaatatcct	12/15/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 ATCCTTGTAA ACTTTGCCCA TATGGTCAGT GTTTTTCAGA GGCAGGTATT TCACAACAAC
 TTTTTAAAAA GAGGTAAAAC TAATCAATCT TACAGATTTG ATCAGCAAAG ATGATCTGGA
 ATATTTAGAA TTAAATTTGT TTAATAAGAA CATTTTggct gggcttggta gctcatgctt
 gtaatcctag cactttggga ggcagaggca ggaggatcac aaaaattagc caggtgtagt
 ggcatgcacc tgtggtccca gctatttggg gaggctgagg tgggaagatg gcctgagccc
 gggaagttga ggctgcagtg agccatgttc tgccactgca cttcagcctg ggtgatagag
 tgagaccctg tctcaaagaa aaaagaaaTT TAACTTACTT TTTGTATAAT TTCTTCAACA
 GCAAATTTAA GG
 Y
 GATACTTATG TCCTCTTCCT GGAATATCCT AAAATTAAGA AAATGTAGTG GAGACAAGAA
 AATATTATAA CAACATTATA CTTGCATTGT TAGAAGTATG CATCTCATTT GGTTGGAGGG
 GCTGGCTGAA GGGGAATGGT GAAAGCCTTA GGTCTTGAAA AAGGCATGTC ACCATGAATG
 TAACATCTAA TTTAGCAAGT

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
sqnm5935 sqnm94233	NT_005612 AA418478 AA436375 BC005346 Hs.109276

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss14195380	CEPH		184	AF					0.450		0.550

	HapMap-CEU	European	120	IG	0.317	0.550	0.133	0.294	0.592		0.408

	HapMap-HCB	Asian	90	IG	0.111	0.422	0.467	1.000	0.322		0.678

	HapMap-JPT	Asian	88	IG	0.182	0.545	0.273	0.527	0.455		0.545

	HapMap-YRI	Sub-Saharan African	120	IG	0.517	0.433	0.050	0.439	0.733		0.267

	CHMJ	Asian	74	IG					0.284	0.014	0.703

ss24381862	AFD_EUR_PANEL	European	48	IG	0.417	0.458	0.125	1.000	0.646		0.354

	AFD_AFR_PANEL	African American	46	IG	0.565	0.304	0.130	0.251	0.717		0.283

	AFD_CHN_PANEL	Asian	48	IG	0.083	0.208	0.708	0.150	0.188		0.812

ss48411522	AGI_ASP population	multiple	28	IG	0.500	0.286	0.214	0.200	0.643		0.357

ss66404026	HapMap-CEU	European	118	GF	0.305	0.593	0.102		0.602		0.398

	HapMap-HCB	Asian	90	GF	0.111	0.422	0.467		0.322		0.678

	HapMap-JPT	Asian	90	GF	0.178	0.533	0.289		0.444		0.556

	HapMap-YRI	Sub-Saharan African	120	GF	0.517	0.433	0.050		0.733		0.267

ss68880540	HapMap-CEU	European	120	GF	0.317	0.583	0.100		0.608		0.392

	HapMap-HCB	Asian	90	GF	0.111	0.422	0.467		0.322		0.678

	HapMap-JPT	Asian	90	GF	0.178	0.533	0.289		0.444		0.556

	HapMap-YRI	Sub-Saharan African	120	GF	0.517	0.433	0.050		0.733		0.267

ss76155823	ICMHP		4	IG	1.000				1.000

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss14195380	1203	427	524	223
ss24381862	71	25	23	23
ss48411522	31
ss66404026	265
ss68880540	266	92	126	48
ss76155823	6

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs8455	1298	455	550	249

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
335	ss14195380	C/T	CSHL-HAPMAP	HapMap-CEU	NA12707	CEPH1358.01	r27_ch3_CEU_affymetrix:genomewidesnp_6.0
335	ss66404026	A/G	CSHL-HAPMAP	HapMap-CEU	NA12707	CEPH1358.01	chr3-HapMap-CEU
335	ss68880540	C/T	CSHL-HAPMAP	HapMap-CEU	NA12707	CEPH1358.01	chr3-HapMap-CEU
361	ss14195380	C/T	CSHL-HAPMAP	HapMap-CEU	NA11993	CEPH1362.14	r27_ch3_CEU_affymetrix:genomewidesnp_6.0
361	ss66404026	A/G	CSHL-HAPMAP	HapMap-CEU	NA11993	CEPH1362.14	chr3-HapMap-CEU
361	ss68880540	C/T	CSHL-HAPMAP	HapMap-CEU	NA11993	CEPH1362.14	chr3-HapMap-CEU
429	ss14195380	C/T	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r27_ch3_CEU_affymetrix:genomewidesnp_6.0
429	ss66404026	A/G	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr3-HapMap-CEU
429	ss68880540	C/T	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr3-HapMap-CEU
439	ss14195380	C/T	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	r27_ch3_CEU_affymetrix:genomewidesnp_6.0
439	ss66404026	A/G	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	chr3-HapMap-CEU
439	ss68880540	C/T	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	chr3-HapMap-CEU

Genotype data submitted for	1313	samples from	1298	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
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .