Reference SNP(refSNP) Cluster Report: rs6540

Reference SNP(refSNP) Cluster Report: rs6540

refSNP ID: rs6540
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/129
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_002817.3:c.*49G>A
NM_175932.2:c.*49G>A
NT_035113.6:g.192649G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38712090 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6540 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
ss8203	CGAP-GAI\|47643	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	08/23/99	10/10/03	52	cDNA	99 %
ss1515496	LEE\|169088	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	09/13/00	10/10/03	86	cDNA	unknown
ss4155925	SC_JCM\|AC069287.5_194578	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	10/15/01	05/16/04	101	Genomic	unknown
ss4392096	LEE\|ge169088	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	04/25/02	10/10/03	106	cDNA	unknown
ss4408321	LEE\|e169088	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	04/26/02	10/10/03	106	cDNA	unknown
ss5004046	YUSUKE\|IMS-JST178137	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	08/12/02	10/10/03	108	Genomic	unknown
ss16258678	CGAP-GAI\|1517407	rev/B	C/T	gtctgagcagccagcttcattggctgcaaa	gcctctctcaggtgagtcaaaggagacacg	11/18/03	11/22/03	120	cDNA	unknown
ss19902141	CSHL-HAPMAP\|CSHL-HuFF-200402.chr11.NT_035113.5_192649	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	02/21/04	03/04/04	120	Genomic	unknown
ss24117566	PERLEGEN\|afd4585272	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	08/10/04	09/13/04	123	Genomic	unknown
ss38712090	ABI\|hCV349611	rev/B	C/T	gtctgagcagccagcttcattggctgcaaa	gcctctctcaggtgagtcaaaggagacacg	07/16/05	11/02/06	126	Genomic	unknown
ss65735155	ILLUMINA\|Human1-rs6540	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	10/10/06	10/10/06	127	Genomic	unknown
ss69306263	PERLEGEN\|PGP04585272	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	01/30/07	08/14/07	127	Genomic	unknown
ss74856385	ILLUMINA\|ILMN_Human_1M_rs6540	fwd/T	A/G	cgtgtctcctttgactcacctgagagaggc	tttgcagccaatgaagctggctgctcagac	08/28/07	08/29/07	129	Genomic	unknown
ss76810805	AFFY\|AFFY_6_1M_SNP_A-8672365	rev/B	C/T	cttcattggctgcaaa	gcctctctcaggtgag	08/28/07	08/30/07	130	Genomic	unknown

Fasta sequence (Legend)

 CCCGTCCCAC TCCCCCAGCT CAGAGGTCCT TTTTACTAGA GCTGCCCTAG AGAGTTAGCT
 GGAGATGTAG AGTCACCCCA TCAGGTGCTG TGCCGGCCGC TCGGCCTGTG TCTCCTGCGT
 GTCTTAACGT CCCTTGTGTC CGGATTTCCA TTTCAGATCA AGGGAATGAA GGACCGCCTG
 GAGTTCTGGT GCACGGATGT GAAGAGCATG GAGATGCTGG TGGAGCACCA GGCCCATGAC
 ATCCTCACCT AGGGCCCCCT GGTTCCCCGT CGTGTCTCCT TTGACTCACC TGAGAGAGGC
 R
 TTTGCAGCCA ATGAAGCTGG CTGCTCAGAC GGTCGACATT GAATTTGGGT GGGGGTTGGG
 ATCCTGTCTG AAGTACAGAC TGTTCTTGCT CTAAAAACAG GACTGTCCCT GATGGGAGCC
 AGGCCACAGG GAGGAGGCTT CTTTGTGGGT CTCTCCTGCA GAGGGTGGGG GTCTCAGGGT
 CTTAGGTGAT ACGGGAGAGA AAGAACGTGC CAGGCAGGAG GCCCCCTGAA GTCTGTGTAC
 TCCGAGGTGG ATCTCCATCC CCATCCACCT GTACGGACAT CTTTTCCGTT GCGGTTTGAG

GeneView

GeneView via analysis of contig annotation: PSMD13 proteasome (prosome, macropain) 26S subunit, non-ATPase, 13

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_035113->NM_002817

function

reference

NT_035113->NM_175932

function

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


reference	NT_035113->NM_002817->	192649	forward	1422	3' UTR

reference	NT_035113->NM_175932->	192649	forward	1428	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6540 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_001838015.1	72317	72317	plus	G	alt_assembly_8	HuRef	HuRef	view	300
11	NT_035113.6	192649	242649	plus	G	ref_assembly	reference	reference	view	300
11	NW_924951.1	105586	306522	minus	C	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
W57859 AA580076 AF015416 Hs.18700 NM_002817

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:
NM_002817.3 NM_175932.2	AF015416.1 AP006566.1	AP006283.1

UniGene Cluster ID
134688

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24117566	AFD_EUR_PANEL	European	48	IG		0.083	0.917	1.000	0.042	0.958

	AFD_AFR_PANEL	African American	42	IG	0.095	0.381	0.524	1.000	0.286	0.714

	AFD_CHN_PANEL	Asian	48	IG	0.167	0.458	0.375	1.000	0.396	0.604

ss38712090	HapMap-CEU	European	120	IG		0.133	0.867	0.584	0.067	0.933

	HapMap-HCB	Asian	86	IG	0.209	0.419	0.372	0.371	0.419	0.581

	HapMap-JPT	Asian	88	IG	0.159	0.455	0.386	1.000	0.386	0.614

	HapMap-YRI	Sub-Saharan African	118	IG		0.373	0.627	0.100	0.186	0.814

ss4155925	CEPH		184	AF					0.030	0.970

ss69306263	HapMap-CEU	European	120	GF		0.133	0.867		0.067	0.933

	HapMap-HCB	Asian	90	GF	0.200	0.422	0.378		0.411	0.589

	HapMap-JPT	Asian	90	GF	0.067	0.489	0.444		0.311	0.689

	HapMap-YRI	Sub-Saharan African	120	GF		0.350	0.650		0.175	0.825

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss24117566	71	6	21	42
ss38712090	259
ss69306263	259	13	79	167

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs6540	332	19	99	201

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5159	ss38712090	C/T	CSHL-HAPMAP	HapMap-HCB	NA18542	CH18542	r23_ch11_HCB_perlegen:genotyping_1.0.0	4379099
5159	ss69306263	G/G	CSHL-HAPMAP	HapMap-HCB	NA18542	CH18542	chr11-HapMap-HCB
5164	ss38712090	C/T	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	r23_ch11_HCB_perlegen:genotyping_1.0.0	4379099
5164	ss69306263	G/G	CSHL-HAPMAP	HapMap-HCB	NA18550	CH18550	chr11-HapMap-HCB
5165	ss38712090	C/C	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	r23_ch11_HCB_perlegen:genotyping_1.0.0	4379099
5165	ss69306263	A/G	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	chr11-HapMap-HCB
5201	ss38712090	T/T	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	r23_ch11_JPT_perlegen:genotyping_1.0.0	4379099
5201	ss69306263	A/G	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	chr11-HapMap-JPT
5206	ss38712090	T/T	CSHL-HAPMAP	HapMap-JPT	NA18968	JA18968	r23_ch11_JPT_perlegen:genotyping_1.0.0	4379099
5206	ss69306263	A/G	CSHL-HAPMAP	HapMap-JPT	NA18968	JA18968	chr11-HapMap-JPT
5209	ss38712090	T/T	CSHL-HAPMAP	HapMap-JPT	NA18960	JA18960	r23_ch11_JPT_perlegen:genotyping_1.0.0	4379099
5209	ss69306263	A/G	CSHL-HAPMAP	HapMap-JPT	NA18960	JA18960	chr11-HapMap-JPT
5227	ss38712090	T/T	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	r23_ch11_JPT_perlegen:genotyping_1.0.0	4379099
5227	ss69306263	A/G	CSHL-HAPMAP	HapMap-JPT	NA18991	JA18991	chr11-HapMap-JPT
5229	ss38712090	C/T	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	r23_ch11_JPT_perlegen:genotyping_1.0.0	4379099
5229	ss69306263	G/G	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	chr11-HapMap-JPT
5236	ss38712090	C/T	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	r23_ch11_JPT_perlegen:genotyping_1.0.0	4379099
5236	ss69306263	G/G	CSHL-HAPMAP	HapMap-JPT	NA19003	JA19003	chr11-HapMap-JPT
5240	ss38712090	C/T	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	r23_ch11_YRI_perlegen:genotyping_1.0.0	4379099
5240	ss69306263	G/G	CSHL-HAPMAP	HapMap-YRI	NA18504	YOR005.03	chr11-HapMap-YRI
5299	ss38712090	C/T	CSHL-HAPMAP	HapMap-YRI	NA19116	YOR060.02	r23_ch11_YRI_perlegen:genotyping_1.0.0	4379099
5299	ss69306263	G/G	CSHL-HAPMAP	HapMap-YRI	NA19116	YOR060.02	chr11-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

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 .