Reference SNP(refSNP) Cluster Report: rs633271

Reference SNP(refSNP) Cluster Report: rs633271

refSNP ID: rs633271
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
Map to Genome Build:	36.3

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

HGVS Names
NM_005387.4:c.948+199G>T
NM_016320.3:c.948+199G>T
NM_139131.2:c.948+199G>T
NM_139132.2:c.948+199G>T
NT_009237.17:g.2576853C>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16520081 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs633271 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
ss805898	SC_JCM\|AC018803.2_83459	fwd/B	G/T	gtctcgctctgtcacccaggctgtagtgca	tggcccagtctcagctcactgcaagctccg	07/27/00	10/10/03	83	Genomic	unknown
ss16110612	SC_SNP\|NT_009237.16_2553552	rev/T	A/C	cggagcttgcagtgagctgagactgggcca	tgcactacagcctgggtgacagagcgagac	11/18/03	11/22/03	120	Genomic	unknown
ss16520081	CSHL-HAPMAP\|CSHL-HuAA-200402.chr11.NT_009237.16_2553552	rev/T	A/C	cggagcttgcagtgagctgagactgggcca	tgcactacagcctgggtgacagagcgagac	02/17/04	08/05/04	120	Genomic	unknown
ss39991631	ABI\|hCV26078925	rev/T	A/C	cggagcttgcagtgagctgagactgggcca	tgcactacagcctgggtgacagagcgagac	07/16/05	07/16/05	126	Genomic	unknown
ss78807445	HGSV\|Cor18507_SNV_20070510.chr11_3746188	rev/T	A/C	cggagcttgcagtgagctgagactgggcca	tgcactacagcctgggtgacagagcgagac	10/19/07	10/20/07	129	Genomic	unknown
ss114111875	1000GENOMES\|NA19240_2008_12_16_2230980_chr11_3746188	rev/T	A/C	cggagcttgcagtgagctgagactgggcca	tgcactacagcctgggtgacagagcgagac	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 ACTGGCTTTT CCTTTGGTAA TACCAGCACC ATAGGACAGC CAAGCACCAA CACCATGGTA
 AGGAAACAGA CCCTTACTTA CCTCCATGTC TTATTTTTAG AGTTAAGTAA TGAGGATTCT
 AATCATGTCA AACTAGCAAA TTCTACCTGT ACTGCAAATC TTAAGAGTTG AGGGTATTTA
 ATGAAGGGAA GAGAACAAAG tttttttttt tttttttgag atggagtctc gctctgtcac
 ccaggctgta gtgca
 K
 tggcccagtc tcagctcact gcaagctccg cctcccaggt tcatgccatt ctcctgcctc
 agcctcccga gtagctggga ctacaggtgt ccaccaccat gtccagctaa ttttttgtgt
 ttttagtaca gatggggttt caccgtgttt gccaggatgg tctcgatctc ctgacctcgt
 gatccgccca cctcggcctc ccaaagtgct gggattatag gcatgagcca ccgtgcccgg
 ccAAGAACAA AGTCTTAGAA TAATTAAGAC CTAGATTCTA GCCTGGGCTC TACTCTTTAC
 TTGTTGAGAT GCTATTGAGG CGATCACTTA TCCTTTCTGA AAGTATTTTT CTCATTACTA
 AGTAGGAACT ACTTAGTGGG CTGGACTTGG CCCTCTTAAA GCTATACCTT GGAAAATTGA
 CTACAGCCAT TCTATAGGGT ATAGGAGAAA ATACTTATTC ATTACTGACT ATATTTCAGA
 ATATAGCCAA CAACAGGAAC

GeneView

GeneView via analysis of contig annotation: NUP98 nucleoporin 98kDa

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_009237->NM_005387

function

reference

NT_009237->NM_016320

function

reference

NT_009237->NM_139131

function

reference

NT_009237->NM_139132

function

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


reference	NT_009237->NM_005387->NP_005378	2576853	reverse	intron

reference	NT_009237->NM_016320->NP_057404	2576853	reverse	intron

reference	NT_009237->NM_139131->NP_624357	2576853	reverse	intron

reference	NT_009237->NM_139132->NP_624358	2576853	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs633271 maps exactly once on NCBI human chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NW_001838018.2	487206	3523478	plus	G	alt_assembly_8	HuRef	HuRef	view	255
11	NT_009237.17	2576853	3746188	minus	C	ref_assembly	reference	reference	view	255
11	NW_924962.1	3374592	3794836	minus	C	alt_assembly_1	Celera	Celera	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
NT_009237 AC060812

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss16520081	HapMap-CEU	European	120	IG	0.633	0.333	0.033	0.752	0.800	0.200

	HapMap-HCB	Asian	90	IG	0.600	0.333	0.067	0.655	0.767	0.233

	HapMap-JPT	Asian	88	IG	0.500	0.386	0.114	0.584	0.693	0.307

	HapMap-YRI	Sub-Saharan African	120	IG	0.233	0.633	0.133	0.050	0.550	0.450

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.421+/-0.182	270	210	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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .