Reference SNP(refSNP) Cluster Report: rs6774540

Reference SNP(refSNP) Cluster Report: rs6774540

refSNP ID: rs6774540
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/129
Map to Genome Build:	36.3

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

HGVS Names
NM_015562.1:c.835-2353A>G
NT_029928.12:g.711645T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10034618 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6774540 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
ss10034618	BCM_SSAHASNP\|chr3.NT_029928.10_711645	fwd/B	C/T	gtggccatggcagacactgtcaggctccta	tgaatttcattctcctctgatttccttact	06/27/03	03/31/08	116	Genomic	unknown
ss14205532	BCM_SSAHASNP\|chr3.NT_029928.11_711645	fwd/B	C/T	gtggccatggcagacactgtcaggctccta	tgaatttcattctcctctgatttccttact	11/05/03	11/22/03	119	Genomic	unknown
ss24645020	PERLEGEN\|afd4443063	fwd/B	C/T	gtggccatggcagacactgtcaggctccta	tgaatttcattctcctctgatttccttact	08/10/04	09/13/04	123	Genomic	unknown
ss44404769	ABI\|hCV1795474	fwd/B	C/T	gtggccatggcagacactgtcaggctccta	tgaatttcattctcctctgatttccttact	07/18/05	07/18/05	126	Genomic	unknown
ss66408692	AFFY\|SNP_A-2111038	rev/T	A/G	aggagaatgaaattca	taggagcctgacagtg	10/29/06	03/31/08	127	Genomic	unknown
ss76164424	AFFY\|AFFY_6_1M_SNP_A-2111038	rev/T	A/G	aggagaatgaaattca	taggagcctgacagtg	08/28/07	08/30/07	130	Genomic	unknown
ss82684662	HGSV\|Cor18555_SNV_20070510.chr3_197580221	fwd/B	C/T	gtggccatggcagacactgtcaggctccta	tgaatttcattctcctctgatttccttact	11/27/07	12/03/07	130	Genomic	unknown
ss85377529	HGSV\|Cor18517_SNV_20070510.chr3_197580221	fwd/B	C/T	gtggccatggcagacactgtcaggctccta	tgaatttcattctcctctgatttccttact	12/06/07	12/09/07	130	Genomic	unknown

Fasta sequence (Legend)

 AGCAAAAAAT TAAAGGGAAA AACAtttttt tgctggttgt tttttttttt tgagagaggt
 tctactctgt cacccaggct gaagtgcagt ggcacaatct cagctcacta ctatctccac
 ctgccaggct caagcaatcc tcccacctca gcctcccaag tagctgggat tacaggcaca
 caccaccaca cccggccaaA GGAAAATTTT AAAGTAAACT TCAGGCGAAC TTACCACCCC
 TAAAAAGCAA GTAGAGGTGT CTATGTGACA TGCAATGGCT TAGGTGGATT GTAAATTTAT
 AGCAATGACA TTGCACATAT AGCATGTAGC TCGATTTTAA AAATTGTGGC CATGGCAGAC
 ACTGTCAGGC TCCTA
 Y
 TGAATTTCAT TCTCCTCTGA TTTCCTTACT TATATAACCC TATTTAAGTT TATAAAACGT
 GTTCAACTAA AAAATTCATT TTACTAATTT CTCTTGTAGC TAGAAAATAG TATTGagcaa
 tagcaattct tatcgaaaaa ttatagaatt aaatgcttat attagaagag agaaaggtat
 caaattaatg acctaagctt ccccacctta aaaaaaaaaa aaaaaagagt atacatccag
 gaaaagaaaa taaaattaag ctcaaagaaa acacaaatta ataaatgacc tagaaagcaa
 atacaataga gaaaaacaaa aaaaACCCAC CAAAATCCCA AGAGCAGTTT Tttgttttgt
 tttgtttttt gtttcttaag agacagagtc ttactgttgc ccaaagactg gagtgcagtg
 actactcaca ggtatgatca tagcacacta cattcctgaa ctcctgggct caagcaatat
 tcctgccaag cagatgggac tataggcaca tgccacACCC CAGCTGGTTC CGTAAGATCA
 ATAAAACTAC TAAGCCTCTG GCCAGACAGT C

GeneView

GeneView via analysis of contig annotation: UBXN7 UBX domain protein 7

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_029928->NM_015562

function

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


reference	NT_029928->NM_015562->NP_056377	711645	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs6774540 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_001838889.1	420919	193389168	plus	C	alt_assembly_8	HuRef	HuRef	view	375
3	NW_921873.1	353577	194672097	plus	T	alt_assembly_1	Celera	Celera	view	375
3	NT_029928.12	711645	197576308	plus	T	ref_assembly	reference	reference	view	375

NCBI Resource Links

Submitter-Referenced
GenBank
NT_029928

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss10034618	HapMap-CEU	European	120	IG	0.283	0.533	0.183		0.550	0.450

	HapMap-HCB	Asian	90	IG	0.756	0.200	0.044		0.856	0.144

	HapMap-JPT	Asian	90	IG	0.800	0.200			0.900	0.100

	HapMap-YRI	Sub-Saharan African	120	IG	0.300	0.467	0.233		0.533	0.467

ss24645020	AFD_EUR_PANEL	European	48	IG	0.250	0.500	0.250	1.000	0.500	0.500

	AFD_AFR_PANEL	African American	46	IG	0.217	0.435	0.348	0.584	0.435	0.565

	AFD_CHN_PANEL	Asian	48	IG	0.542	0.375	0.083	1.000	0.729	0.271

ss66408692	HapMap-CEU	European	118	GF	0.288	0.475	0.237		0.525	0.475

	HapMap-HCB	Asian	90	GF	0.756	0.200	0.044		0.856	0.144

	HapMap-JPT	Asian	90	GF	0.800	0.200			0.900	0.100

	HapMap-YRI	Sub-Saharan African	120	GF	0.300	0.467	0.233		0.533	0.467

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss10034618	267	121	109	37
ss24645020	71	24	31	16
ss66408692	266

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs6774540	332	142	136	51

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
170	ss10034618	C/T	CSHL-HAPMAP	HapMap-CEU	NA07000	CEPH1340.10	r23_ch3_CEU_affymetrix:genechip500k
170	ss66408692	A/A	CSHL-HAPMAP	HapMap-CEU	NA07000	CEPH1340.10	chr3-HapMap-CEU
265	ss10034618	C/T	CSHL-HAPMAP	HapMap-CEU	NA11832	CEPH1350.13	r23_ch3_CEU_affymetrix:genechip500k
265	ss66408692	A/A	CSHL-HAPMAP	HapMap-CEU	NA11832	CEPH1350.13	chr3-HapMap-CEU
439	ss10034618	C/T	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	r23_ch3_CEU_affymetrix:genechip500k
439	ss66408692	A/A	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	chr3-HapMap-CEU

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	269

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 .