Reference SNP(refSNP) Cluster Report: rs756648

Reference SNP(refSNP) Cluster Report: rs756648

refSNP ID: rs756648
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_173793.3:c.*303C>T
NT_011519.10:g.2583635G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss7991821 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs756648 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
ss128208	TSC-CSHL\|TSC0100342	fwd/B	C/T	tcaggctgggcatggtagcataggagatgg	ggtcctgaggtctaggcttctcaggtaaac	09/06/00	10/10/03	86	Genomic	95 %
ss3203921	YUSUKE\|IMS-JST024005	rev/T	A/G	gtttacctgagaagcctagacctcaggacc	ccatctcctatgctaccatgcccagcctga	09/05/01	10/10/03	100	Genomic	unknown
ss7991821	SC_SNP\|NT_011519.9_2579366	rev/T	A/G	gtttacctgagaagcctagacctcaggacc	ccatctcctatgctaccatgcccagcctga	04/15/03	05/16/04	114	Genomic	unknown
ss16247311	CGAP-GAI\|1492742	fwd/B	C/T	tcaggctgggcatggtagcataggagatgg	ggtcctgaggtctaggcttctcaggtaaac	11/18/03	11/22/03	120	cDNA	unknown
ss44329043	ABI\|hCV2618344	rev/T	A/G	gtttacctgagaagcctagacctcaggacc	ccatctcctatgctaccatgcccagcctga	07/18/05	11/03/06	126	Genomic	unknown
ss46557904	PERLEGEN\|PS00105550	rev/T	A/G	gtttacctgagaagcctagacctcaggacc	ccatctcctatgctaccatgcccagcctga	08/01/05	08/01/05	126	Genomic	unknown
ss76761187	AFFY\|AFFY_6_1M_SNP_A-8622663	rev/T	A/G	cctagacctcaggacc	ccatctcctatgctac	08/28/07	08/30/07	130	Genomic	unknown

Fasta sequence (Legend)

 GAGTCCGGGC TGCACGGAAG CACATCCTGG TGTGGGCCCC GAGGCAGAGC CCCCCTCCAG
 ACTGGCATCT CCCTCTGCCA CAGGAGAAGG ACGAGTGACA AGCATCCCTG CCATTGGCCT
 GTGCAGCTTC CTCAGTCTGT TTCAAGTTGC TGTTGCACAG CCCTGGGGAC TGTGACCAGC
 CTACACAGTC TGGTGGGTCC CTGTGAGCTC TTGCTCACAG GAACATGGAG CAGGACATTG
 CTAGCCCTAC TTGCCCACCC CTCACCTGCA TGCAGGATAC CCTGACACTG CGATGTTCTG
 CAGGACAATT GCACCGCTTT AGAGCTTCCA GGAGGCCAAG CATTATGGCA GGTACTTGTG
 AGCAGCCAGG TCAGGCTGGG CATGGTAGCA TAGGAGATGG
 Y
 GGTCCTGAGG TCTAGGCTTC TCAGGTAAAC TGAAGGGTAG CCCTGACCTG TGTGGACACA
 CAGGTGGGTC ATAATGAGGT AGCTAAACAG TTGTGCCACT GTGAATGTCT TTCCTAGTCC
 TTGGGAAACT GCCTGCCACG TCCCAGGTTT GGTGAGCATT GTGAGTGCTC ACACTCTGCT
 CCACTCGCTC AGTTCCACTG CACATGCAGG CAGGTGTGCC GAGCAGGTAG GGCTTGCTGG
 CCCCTCTGCA CCAGCAGGCT TCACTTCTTA GGCTCCCAGG TCGGCCCCTG GAGACTCTGG
 TTTTTAAGAA ATGCACACAG CTACAGAACA CACAACCTTG CATAAAGAGG GTTTGTGGAC
 TCAGCTGAAG AAATCCAAGT CCAAGACATA TGGAATTAAG

GeneView

GeneView via analysis of contig annotation: C22orf39 chromosome 22 open reading frame 39

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_011519->NM_173793

function

HuRef

NW_001838737->NM_173793

function

Celera

NW_927495->NM_173793

function

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


reference	NT_011519->NM_173793->	2583635	reverse	630	3' UTR

HuRef	NW_001838737->NM_173793->	892965	forward	630	3' UTR

Celera	NW_927495->NM_173793->	552970	reverse	630	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs756648 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_001838737.2	892965	3052297	plus	T	alt_assembly_8	HuRef	HuRef	view	400
22	NW_927495.1	552970	3283742	minus	A	alt_assembly_1	Celera	Celera	view	400
22	NT_011519.10	2583635	17811485	minus	G	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011519 BI826040

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank mRNA:
NM_173793.3	AC000068.2 NC_000022.9	BC062599.1

UniGene Cluster ID
474210

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss3203921	JBIC-allele		1294	AF					0.319	0.681

ss44329043	AoD_African_American		90	AF					0.520	0.480

	AoD_Caucasian		92	AF					0.280	0.720

	AoD_Chinese		90	AF					0.260	0.740

	AoD_Japanese		90	AF					0.290	0.710

ss7991821	CEPH		184	AF					0.360	0.640

	HapMap-CEU	European	120	IG	0.467	0.450	0.083		0.692	0.308

	HapMap-HCB	Asian	90	IG	0.533	0.422	0.044		0.744	0.256

	HapMap-JPT	Asian	90	IG	0.400	0.511	0.089		0.656	0.344

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.423+/-0.181	180	150	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .