Reference SNP(refSNP) Cluster Report: rs41113

Reference SNP(refSNP) Cluster Report: rs41113

refSNP ID: rs41113
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	76/129
Map to Genome Build:	36.3

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

HGVS Names
NM_005983.2:c.280+2306G>C
NM_032637.2:c.280+2306G>C
NT_006576.15:g.36128207G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2059319 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs41113 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
ss46502	KWOK\|OVLP-36042	fwd/T	C/G	gttagaaaagcagtagagggttgtagtgaa	tcagatctgggtttgaatcctcattcttgc	04/28/00	10/10/03	76	Genomic	91 %
ss348590	KWOK\|OVLP-000621-108637	fwd/T	C/G	gttagaaaagcagtagagggttgtagtgaa	tcagatctgggtttgaatcctcattcttgc	06/30/00	10/10/03	79	Genomic	99 %
ss613371	SC_JCM\|AC008942.4_110183	fwd/T	C/G	gttagaaaagcagtagagggttgtagtgaa	tcagatctgggtttgaatcctcattcttgc	07/12/00	10/10/03	87	Genomic	unknown
ss1169496	KWOK\|OVLP-000804-538297	fwd/T	C/G	gttagaaaagcagtagagggttgtagtgaa	tcagatctgggtttgaatcctcattcttgc	09/02/00	10/10/03	86	Genomic	99 %
ss1252070	KWOK\|OVLP-000804-540687	fwd/T	C/G	gttagaaaagcagtagagggttgtagtgaa	tcagatctgggtttgaatcctcattcttgc	09/02/00	10/10/03	86	Genomic	97 %
ss2028421	KWOK\|OVLP-000925-660305	fwd/T	C/G	gttagaaaagcagtagagggttgtagtgaa	tcagatctgggtttgaatcctcattcttgc	10/06/00	10/10/03	87	Genomic	99 %
ss2059319	KWOK\|OVLP-000925-663272	fwd/T	C/G	gttagaaaagcagtagagggttgtagtgaa	tcagatctgggtttgaatcctcattcttgc	10/06/00	10/25/06	87	Genomic	97 %
ss66139775	AFFY\|SNP_A-2099571	fwd/T	C/G	agagggttgtagtgaa	tcagatctgggtttga	10/27/06	08/14/07	127	Genomic	unknown
ss76156087	AFFY\|AFFY_6_1M_SNP_A-2099571	fwd/	C/G	agagggttgtagtgaa	tcagatctgggtttga	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 CGAAGAAGAA ACAGATTAAA CATTTAAAGA TGAAGTCTTG CAGACCCAAG GTAATTTAAG
 TATATTCATA AATTCTCCCA TCTGGTTTCC TTTGCAGAAG ggttgataga ttggttgttt
 agttgattgg ttggttgctc gctttggcag cacatatact gaaactggaa atacagagaa
 gattagcatg gcccctgcgc aggaagacat gcggattcga gatgcattcc acttttttAA
 TTAAGAAAAT AAATACGTTT GTTTTCAGCC TTTTCTTTAG GAAAGAGAAC TTTGCCCAAT
 TTATGGTCTG GGAATATACA TCAGGAATTG GATTAGTTAG AAAAGCAGTA GAGGGTTGTA
 Gtgaa
 S
 tcagatctgg gtttgaatcc tcattcttgc gtttatcagc cttggaaagt tattcgagct
 ttctttgcct tagttcctta gtctgtgaaa tggagtgctg taataatacc cacttcacag
 gtcgtcgtga agattaaatg agaatgacgt aaaaccctta gcatgccact gacacgtaac
 aaTACATAAG CCAACAAAAT TCCTGACACC AATTTTGGAG GCTAGTGGAC TTTTATCTTT
 TGTTTTTAAT ATTGTTACTC TGACCCTGTT AGTATAAAAT TTTTTTTCTT CAAAATTTAA
 TGTTCACCGC TCTTCTTTGT GTCTGGAATG TAGCCCTAAC AATCTGGTGC TTGACCAACC
 AAATATGGCG AAAGATACTT CC

GeneView

GeneView via analysis of contig annotation: SKP2 S-phase kinase-associated protein 2 (p45)

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_006576->NM_005983

function

reference

NT_006576->NM_032637

function

HuRef

NW_001838933->NM_005983

function

HuRef

NW_001838933->NM_032637

function

Celera

NW_922596->NM_005983

function

Celera

NW_922596->NM_032637

function

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


reference	NT_006576->NM_005983->NP_005974	36128207	forward	intron

reference	NT_006576->NM_032637->NP_116026	36128207	forward	intron

HuRef	NW_001838933->NM_005983->NP_005974	449202	forward	intron

HuRef	NW_001838933->NM_032637->NP_116026	449202	forward	intron

Celera	NW_922596->NM_005983->NP_005974	1751647	forward	intron

Celera	NW_922596->NM_032637->NP_116026	1751647	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs41113 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_922596.1	1751647	36041133	plus	G	alt_assembly_1	Celera	Celera	view	365
5	NW_001838933.1	449202	36106591	plus	G	alt_assembly_8	HuRef	HuRef	view	365
5	NT_006576.15	36128207	36191207	plus	G	ref_assembly	reference	reference	view	365

NCBI Resource Links

Submitter-Referenced
GenBank
AC025476.3 AC025476 AC025476.3 AC026735 AC026735.3

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC008942.6 NC_000005.8	AC025476.5 AC026735.4

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/G	G/G	HWP	C	G
ss2059319	HapMap-CEU	European	120	IG		1.000			1.000

	HapMap-HCB	Asian	90	IG		1.000			1.000

	HapMap-JPT	Asian	90	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.100	0.900	0.752	0.050	0.950

ss66139775	HapMap-CEU	European	118	GF		1.000			1.000

	HapMap-HCB	Asian	90	GF		1.000			1.000

	HapMap-JPT	Asian	90	GF		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.100	0.900		0.050	0.950

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.028+/-0.115	270	210	269	0

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 .