Reference SNP(refSNP) Cluster Report: rs150594

Reference SNP(refSNP) Cluster Report: rs150594

refSNP ID: rs150594
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:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_004298.2:c.1179T>C
NM_153485.1:c.1356T>C
NP_004289.1:p.A393A
NP_705618.1:p.A452A
NT_006576.15:g.37306483A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1634679 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs150594 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
ss236484	KWOK\|OVLP-000621-233095	rev/B	C/T	aacatttatttcttttacatagatgacagc	ggtgttgatggtcattcctgggctctttct	06/30/00	10/10/03	79	Genomic	94 %
ss281899	KWOK\|OVLP-000621-225358	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	06/30/00	10/10/03	79	Genomic	97 %
ss621985	SC_JCM\|AC025449.3_69718	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	07/12/00	10/10/03	80	Genomic	unknown
ss1262163	KWOK\|OVLP-000804-639367	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	09/02/00	10/10/03	86	Genomic	97 %
ss1277576	KWOK\|OVLP-000804-640039	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	09/02/00	10/10/03	86	Genomic	94 %
ss1634679	KWOK\|OVLP-000925-233982	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	10/04/00	04/07/04	87	Genomic	97 %
ss1653781	KWOK\|OVLP-000925-239647	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	10/05/00	10/10/03	87	Genomic	94 %
ss3438769	SC_JCM\|AC025449.4_103127	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	09/24/01	10/10/03	100	Genomic	unknown
ss11706466	WI_SSAHASNP\|chr5.NT_006576.13_19760472	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	07/03/03	10/10/03	116	Genomic	unknown
ss14677767	WI_SSAHASNP\|chr5.NT_006576.14_19785833	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	11/05/03	11/22/03	119	Genomic	unknown
ss14841095	SC_SNP\|NT_006576.14_19785833	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	11/12/03	11/22/03	119	Genomic	unknown
ss23719827	PERLEGEN\|afd0835879	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	08/10/04	09/13/04	123	Genomic	unknown
ss75049553	ILLUMINA\|ILMN_Human_1M_rs150594	fwd/T	A/G	agaaagagcccaggaatgaccatcaacacc	gctgtcatctatgtaaaagaaataaatgtt	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 CTTATTTTTG TCACTACCAT AACAGAATAC GTACACACCT GTGCTGAGAG GAGAACAAAT
 TTCTTCGGAG GTAACATGTG CTGCTGTACA ACAACTGGTG AATCAGTTAT TGGAATATGA
 TCCTTGTTTA AAGGTGTAAT TATTTTATCT ACTTTCAATT CATCTATCGC AGAAAGAGCC
 CAGGAATGAC CATCAACACC
 R
 GCTGTCATCT ATGTAAAAGA AATAAATGTT TTATACATCA TATTGAAGTT ACATAATGCA
 AAAGAAAAAA CTACAGACTT AATAAAGAAG TAAATTTAAT AAATAGTACA TTAACATGAA
 TATTTTTGAA AGTATTATGT AATTTTCTAC TATCTTTTTT TTAAATCAGG TATTTTCTGG
 Gtttttgttt tttgtttttt ttttgagacg aagttgtcta ggctggagtg tagtggagtg
 atcttggctc actgtaacct ttgcctcccg ggttcaagtg attctcctgc ctcagcctcc
 ctagtagctg ggattacagc catatgtcac cacgcccagc taatttttta tttttagtgg
 ggacggggtt tctccatgtt ggtcaggctg gtcttgaact ctcgacctca ggtgatccgc
 ccacctcggc ctcccaaagc gctgggatta caggcatgag ccaccacacc tggccTCTGG
 GGtttttttt ttttgagaca gcatcttact ctgtcaccta agctggagtg cgctggcacg
 atcacaactc actgcaacct cgacctccct gggttcagct gattctccca cctcaacctc
 ccaagtagct gggactacag gagaatgcta ccacggccgc ctaatttttc tatgttttgt
 atgaacaggg ttttaccatg ttgcccagga tgttctcgaa ctcctgggct catgcagtct
 gcccatcttg gcctctcaaa gtgctAATCA GGCATTACCt tttttttttt tctgaggcag
 agtctcaccc tgttgccaag gctggagtgc agtggcctaa tcagagccca ctgtaacgtc
 tgcttcccag gttcatgcaa ttctcctgcc tcagccttcc gagtatctgg gattagagac
 gcacaccacc atacccggct aatttttgta ttgttattag agactggctt ttgccatgtt
 ggccaggctg gtctcaaact cctgacctca ggtgatctgc ctgccttggc ctctttccaa
 agtgctagga ttacaggcgt gagccaccat gcccagccAT AAGCAGGCAT TTTCTATACT
 AATACATAAA TCTTTTTGTA CTAGAGGACA AGGGCAAACT TTTCTCAAGA TAAACTATAA
 ATACTCTTTA ATAAAATT

GeneView

GeneView via analysis of contig annotation: NUP155 nucleoporin 155kDa

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_004298

function

reference

NT_006576->NM_153485

function

HuRef

NW_001838933->NM_004298

function

HuRef

NW_001838933->NM_153485

function

Celera

NW_922596->NM_004298

function

Celera

NW_922596->NM_153485

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_006576->NM_004298->NP_004289	37306484	reverse	1319	synonymous	C	Ala [A]	3	393
					contig reference	T	Ala [A]	3	393

reference	NT_006576->NM_153485->NP_705618	37306484	reverse	1474	synonymous	C	Ala [A]	3	452
					contig reference	T	Ala [A]	3	452

HuRef	NW_001838933->NM_004298->NP_004289	1628659	reverse	1319	synonymous	C	Ala [A]	3	393
					contig reference	T	Ala [A]	3	393

HuRef	NW_001838933->NM_153485->NP_705618	1628659	reverse	1474	synonymous	C	Ala [A]	3	452
					contig reference	T	Ala [A]	3	452

Celera	NW_922596->NM_004298->NP_004289	2931173	reverse	1319	synonymous	C	Ala [A]	3	393
					contig reference	T	Ala [A]	3	393

Celera	NW_922596->NM_153485->NP_705618	2931173	reverse	1474	synonymous	C	Ala [A]	3	452
					contig reference	T	Ala [A]	3	452

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs150594 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	2931173	37220659	plus	A	alt_assembly_1	Celera	Celera	view	200
5	NW_001838933.1	1628659	37286048	plus	A	alt_assembly_8	HuRef	HuRef	view	200
5	NT_006576.15	37306484	37369484	plus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_006576 AC008832 AF165926 AF165926.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AC025449.6 AF165926.2 NC_000005.8

UniGene Cluster ID
481942

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1634679	CEPH		184	AF					0.850	0.150

	HapMap-CEU	European	120	IG	0.783	0.183	0.033	0.251	0.875	0.125

	HapMap-HCB	Asian	90	IG	0.844	0.156		0.584	0.922	0.078

	HapMap-JPT	Asian	88	IG	0.886	0.114		0.752	0.943	0.057

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

ss23719827	AFD_EUR_PANEL	European	46	IG	0.826	0.174		0.655	0.913	0.087

	AFD_AFR_PANEL	African American	46	IG		0.304	0.696	0.403	0.152	0.848

	AFD_CHN_PANEL	Asian	46	IG	0.870	0.087	0.043	0.050	0.913	0.087

ss621985	SC_12_C	European	12	IG	0.833	0.167		1.000	0.917	0.083

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.444+/-0.158	342	261	11	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA, PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .