Reference SNP(refSNP) Cluster Report: rs364677

Reference SNP(refSNP) Cluster Report: rs364677

refSNP ID: rs364677
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	80/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001033581.1:c.-129-3884A>G
NM_001033582.1:c.-129-3884A>G
NM_002744.4:c.421-3884A>G
NT_004350.18:g.1550394A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1570310 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs364677 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
ss461998	SC_JCM\|AC068198.7_207150	fwd/T	A/G	gctccaaccatcagaataggtaagggtgtg	caggtctaaaacatgaaaatgggcgattga	07/12/00	10/10/03	80	Genomic	unknown
ss978102	KWOK\|OVLP-000804-564948	fwd/T	A/G	gctccaaccatcagaataggtaagggtgtg	caggtctaaaacatgaaaatgggcgattga	09/01/00	10/10/03	86	Genomic	99 %
ss1570310	KWOK\|OVLP-000925-52565	fwd/T	A/G	gctccaaccatcagaataggtaagggtgtg	caggtctaaaacatgaaaatgggcgattga	10/04/00	10/30/04	87	Genomic	99 %
ss2549944	SC_JCM\|AC068198.11_206923	fwd/T	A/G	gctccaaccatcagaataggtaagggtgtg	caggtctaaaacatgaaaatgggcgattga	11/03/00	10/10/03	92	Genomic	unknown
ss16399737	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_004350.16_49427	fwd/T	A/G	gctccaaccatcagaataggtaagggtgtg	caggtctaaaacatgaaaatgggcgattga	02/17/04	03/04/04	120	Genomic	unknown
ss17335030	CSHL-HAPMAP\|CSHL-HuCC-200402.chr1.NT_004350.16_49427	fwd/T	A/G	gctccaaccatcagaataggtaagggtgtg	caggtctaaaacatgaaaatgggcgattga	02/19/04	03/04/04	120	Genomic	unknown
ss44089390	ABI\|hCV1406823	rev/B	C/T	tcaatcgcccattttcatgttttagacctg	cacacccttacctattctgatggttggagc	07/18/05	11/03/06	126	Genomic	unknown
ss84143588	HGSV\|Cor19129_SNV_20070510.chr1_2103927	fwd/T	A/G	gctccaaccatcagaataggtaagggtgtg	caggtctaaaacatgaaaatgggcgattga	12/06/07	12/06/07	130	Genomic	unknown
ss87164311	BCMHGSC_JDW\|JWB-0001400	fwd/T	A/G	gctccaaccatcagaataggtaagggtgtg	caggtctaaaacatgaaaatgggcgattga	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 AAGCAGTGCC CTCAGGTGGC TGGCAGAGGC CAATGCAATT CCTTTTCAAG CCAGCATCAA
 AGAATTCCTG ATGATAAATA AATCAGGCAT CTGAGCTCGC AATGGAAAAC CACAAAACAC
 AGTGGGAAGC AGGATATCCT GAGTCCAAGC TGGTAAAAGC CCAGACAGAG GCTCCAACCA
 TCAGAATAGG TAAGGGTGTG
 R
 CAGGTCTAAA ACATGAAAAT GGGCGATTGA AAATATGAGC AGGAggccgg gcgcggtggc
 tcacgcatgt aatcccagca ctttgggagg ccgaggcagg cggagtgcct gaggtcagga
 gttcgagacc agcctggtca acatagtgaa acactgtctc tactaaaaat acaacaaaaa
 tttagccagg cgtggtggtg ggtgcctgta atcccaggta ctcggtaggc tgaggcaggg
 gaatggcttg aaccagggag ctggaggttt cagtgagctg agaacatgcc actgtactcc
 agcttgggtg acagagtgag actccgtctc aaaaaaaaag aaagaaaaTG TGAGCAGGGA
 ggccaggtgc agtagctcac acctgtaatc ccagcacttt gggaggctgg agcgggcaga
 tcacctgagg tcaggggttc gagacgagcc tggccaacat ggcgaaactt tgtctctact
 aaaaataaaa aatcagccgg acgtggtggc aggtgcctat aatcccagct actcaggagg
 ctgagacagg agaatcgctt gaacccagga ggcggaggct gcagtgagcc aagatcgtac
 cactgcactc cagcctgggg aacagagcga GGCGCGAGGC TGTCGGAGGG AGGGAATATG
 AGCAAGGAAC AAGTTGGCAG CATGTAAGAC GTACTTAAAA CGTTTTTACC CATTAATCTA
 TGAATTCCTC TGAGTTTCTG AGAATGGAAA CTTGGGGTTT AGGTTTTATT TTTTTAA

GeneView

GeneView via analysis of contig annotation: PRKCZ protein kinase C, zeta

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_004350->NM_001033581

function

reference

NT_004350->NM_001033582

function

reference

NT_004350->NM_002744

function

HuRef

NW_001838585->NM_001033581

function

HuRef

NW_001838585->NM_001033582

function

HuRef

NW_001838585->NM_002744

function

Celera

NW_921350->NM_001033581

function

Celera

NW_921350->NM_001033582

function

Celera

NW_921350->NM_002744

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_004350->NM_001033581->NP_001028753	1550394	forward	intron

reference	NT_004350->NM_001033582->NP_001028754	1550394	forward	intron

reference	NT_004350->NM_002744->NP_002735	1550394	forward	intron

HuRef	NW_001838585->NM_001033581->NP_001028753	1328647	forward	intron

HuRef	NW_001838585->NM_001033582->NP_001028754	1328647	forward	intron

HuRef	NW_001838585->NM_002744->NP_002735	1328647	forward	intron

Celera	NW_921350->NM_001033581->NP_001028753	521010	reverse	intron

Celera	NW_921350->NM_001033582->NP_001028754	521010	reverse	intron

Celera	NW_921350->NM_002744->NP_002735	521010	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs364677 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_921350.1	521010	521010	minus	T	alt_assembly_1	Celera	Celera	view	200
1	NW_001838585.1	1328647	1347894	plus	G	alt_assembly_8	HuRef	HuRef	view	200
1	NT_004350.18	1550394	2061625	plus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_004350 AL162271 AL162271.3 AL162271.4

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL162271.11 NC_000001.9	AC068198.11

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1570310	HapMap-CEU	European	120	IG	0.167	0.450	0.383	0.752	0.392	0.608

	HapMap-HCB	Asian	90	IG	0.022	0.467	0.511	0.150	0.256	0.744

	HapMap-JPT	Asian	88	IG	0.023	0.341	0.636	0.584	0.193	0.807

	HapMap-YRI	Sub-Saharan African	120	IG	0.217	0.383	0.400	0.150	0.408	0.592

ss44089390	AoD_African_American		90	AF					0.300	0.700

	AoD_Caucasian		92	AF					0.280	0.720

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.439+/-0.164	270	210	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .