Reference SNP(refSNP) Cluster Report: rs282179

Reference SNP(refSNP) Cluster Report: rs282179

refSNP ID: rs282179
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_001006665.1:c.*43C>G
NM_002953.3:c.*43C>G
NT_004610.18:g.9725077C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss71646443 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs282179 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
ss365764	KWOK\|OVLP-000621-152152	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	06/30/00	10/10/03	79	Genomic	99 %
ss549051	SC_JCM\|AL109743.3_10358	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	07/12/00	05/16/04	80	Genomic	unknown
ss1176644	KWOK\|OVLP-000804-571124	fwd/B	C/G	ggcctgctccctctgggaagcatgctgact	tgtcaagctagcaccgccctgtggcccgaa	09/02/00	10/10/03	86	Genomic	99 %
ss1536214	LEE\|671674	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	09/13/00	10/10/03	86	cDNA	unknown
ss1887813	KWOK\|OVLP-000925-278952	fwd/B	C/G	ggcctgctccctctgggaagcatgctgact	tgtcaagctagcaccgccctgtggcccgaa	10/06/00	10/10/03	87	Genomic	99 %
ss1888027	KWOK\|OVLP-000925-280720	fwd/B	C/G	ggcctgctccctctgggaagcatgctgact	tgtcaagctagcaccgccctgtggcccgaa	10/06/00	10/10/03	87	Genomic	99 %
ss3176762	WICVAR\|WIAF-16625	rev/T	C/G	ttcrggccacagggcggtgctagcttgaca	agtcagatgcttccagagggagcaggccgg	06/28/01	04/07/04	98	cDNA	unknown
ss3190339	YUSUKE\|IMS-JST016250	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	08/07/01	10/10/03	98	Genomic	unknown
ss4322172	CGAP-GAI\|257740	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	11/28/01	10/10/03	102	cDNA	unknown
ss4424518	LEE\|e671675	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	04/26/02	10/10/03	106	cDNA	unknown
ss6879671	WI_SSAHASNP\|NT_037485.1_61927	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	02/12/03	10/10/03	111	Genomic	unknown
ss13043939	SC_SNP\|NT_037485.3_1011944	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	10/22/03	10/31/03	119	Genomic	unknown
ss16243251	CGAP-GAI\|1483799	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	11/18/03	11/22/03	120	cDNA	unknown
ss16416321	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_037485.3_1011944	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	02/17/04	03/04/04	120	Genomic	unknown
ss19847740	CSHL-HAPMAP\|CSHL-HuFF-200402.chr1.NT_037485.3_1011944	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	02/21/04	03/04/04	120	Genomic	unknown
ss20547419	SSAHASNP\|WGSA-200403-chr1.chr1.NT_037485.3_1011944	rev/T	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	03/18/04	03/18/04	121	Genomic	unknown
ss44132154	ABI\|hCV3049350	rev/	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	07/18/05	07/18/05	126	Genomic	unknown
ss71646443	SI_EXO\|NT_004610.18_9725077	rev/	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	05/07/07	05/07/07	127	Genomic	unknown
ss81565499	HGSV\|Cor18555_SNV_20070510.chr1_26584877	rev/	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	11/27/07	11/30/07	130	Genomic	unknown
ss87317449	BCMHGSC_JDW\|JWB-0027006	rev/	C/G	ttcgggccacagggcggtgctagcttgaca	agtcagcatgcttcccagagggagcaggcc	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGGACTGTCT CGGAGGTGTG TGCAGATGGC TACAGGTGGC CAATCGTGGG GGTCCCCAGG
 GTGGGATCCC AAAGCTGCTC TAAAGAGTCT CAGAGAGCCC CAGCGTGACT CAGTTCCCCT
 CCTGGGGCCG CAATGGCTGT TTCTGCTCCC AGAAAGGCAA ATGGATCTTG TAAAAATCCA
 TGGTGGTTGA TGCCATTTTT TTCATAAAAA AAAGTTTATA CAGTGAATCG CTTTCCACCA
 GCAGAGCCTG AGCCGAGAAG AGTCCATCCT GGGGAAGGAG AAGGCACTTC TCACACCCTC
 ATTAGGGGTG TTCTGGGCTG GCAGCTTCCC CGGCCCCTCG GGTTCCAGCT CCCTCTGGCC
 CTGTGGTTCC GGCCTGCTCC CTCTGGGAAG CATGCTGACT
 S
 TGTCAAGCTA GCACCGCCCT GTGGCCCGAA TGCCCTGGTG CCTCACAGGG TGGTGGATGG
 CAACTTCCTC ACTCGCCGCT GGGCCAGGAT GGATGACTCG ATGGGCTTCA GCTGGGGGGT
 GGGCTTGGAG CTGTTGAGTG CGGAGTACGT GGCAGCCATG GCTCCCTGAA AGAGAAGTGG
 GGAGGTCAGG TCACAATGGT GGGAGATGTA GCGGGGAGGG GATCCATGCC CCAAGGGTAG
 GCCAGCCCCT CTCAGTGTTC CACAGCCCAC TTTTTTTGGT TTTGTTTTTG TTGTTTTTTT
 TTTTTTGAGA TACAGTCTCA CTCTGTCACC CAGGCTGGAA CGCAATGGCA CAATCTTGGC
 TCACTGCAAC CTCTGCCCCC AGGGTTCAAG CGATTCTCCT

GeneView

GeneView via analysis of contig annotation: RPS6KA1 ribosomal protein S6 kinase, 90kDa, polypeptide 1

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_004610->NM_001006665

function

reference

NT_004610->NM_002953

function

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


reference	NT_004610->NM_001006665->	9725077	forward	2327	3' UTR

reference	NT_004610->NM_002953->	9725077	forward	2414	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs282179 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_001838576.1	799824	25155002	minus	C	alt_assembly_8	HuRef	HuRef	view	400
1	NW_921351.1	1158785	25297927	minus	G	alt_assembly_1	Celera	Celera	view	400
1	NT_004610.18	9725077	26773322	minus	C	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
CGAP-C-25774	NT_037485 AA479556 AC020723 AL109743.3 AL139224.6 Hs.149957

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:
NM_001006665.1 NM_002953.3	AL109743.4 AL627313.16	AL139224.8

UniGene Cluster ID
149957

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss3176762	MITOGPOP6	multiple	50	IG	0.680	0.160	0.160	0.010	0.760	0.240

ss3190339	JBIC-allele		1486	AF					0.792	0.208

ss549051	CEPH		184	AF					0.840	0.160

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.365+/-0.222	25	25	0	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, NCBI

UNKNOWN

YES

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Revised: May 25, 2006 1:38 PM .