Reference SNP(refSNP) Cluster Report: rs5765304

Reference SNP(refSNP) Cluster Report: rs5765304

Linkout query returns no result.

refSNP ID: rs5765304
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	114/129
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_148674.3:c.2059-3802C>T
NT_011523.11:g.1042680G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8019772 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs5765304 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss8019772	SC_SNP\|NT_011522.3_1031255		fwd/T	A/G	ccatttttatttggctagtcaagcatagtc	tgagagctttaccatttctaagtgtacagt	04/15/03	10/30/04	114	Genomic			unknown
ss76518245	AFFY\|AFFY_6_1M_SNP_A-8379309		rev/B	C/T	aatggtaaagctctca	gactatgcttgactag	08/28/07	08/30/07	129	Genomic			unknown

Fasta sequence (Legend)

 TACATATGAT GACATGACTT TTCTCCTGCC TTTAATTCAT TAATAGATTA TGATGATCAC
 TTAAACACCC TTGTATTTGT GAAATAAATT CTATCTAGTC AGATGTATTA TTTTACTACA
 GTGTTCAATT CTCTAATACT GACATTTAGA TATTATATAT TTATACTCAT AAGGGAAGTC
 AGTTTTTAGT TTTATTTTTT GTACTATATA TTTTATATTA AAGTTATACT ACCTTTATAA
 AATAAGCTGG AAAGTTTCCA TCTTTTTTAT ATGTTACAta gaactgagct gtaagcccat
 ctggtcccag aggttatttt tggtttttac ttgtggtaaa atatacgtaa cataaaattt
 accatcgtta ccatttttat ttggctagtc aagcatagtc
 R
 tgagagcttt accatttcta agtgtacagt tcagtagtgt ttaaatatat ccacattgtg
 tgcaagcaat ctccagatct cttcatcttc caaaactgaa actctgtctc acttaaacaa
 caactcattc tctccccttc tacagccact ggcaaccact ggcctccttt ctgtctctta
 tgaattggac tactctaggt acctcatgtt agtggaatca gacagtattt gtcttcaagt
 ttcatctatg ttgtagcata tgccacaatt tcctccattt ttaatgctga ataatattcc
 attgtatgta tataccacat tctgtttatc cattcatctg ttgattgaca cctggattgc
 ttctaccttt tggctattgt gaataatgct gctatgaaca

GeneView

GeneView via analysis of contig annotation: SMC1B structural maintenance of chromosomes 1B

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_011523->NM_148674

function

HuRef

NW_001838751->NM_148674

function

Celera

NW_927650->NM_148674

function

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


reference	NT_011523->NM_148674->NP_683515	1042680	reverse	intron

HuRef	NW_001838751->NM_148674->NP_683515	296319	reverse	intron

Celera	NW_927650->NM_148674->NP_683515	2862994	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs5765304 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_001838751.1	296319	28718083	plus	G	alt_assembly_8	HuRef	HuRef	view	400
22	NW_927650.1	2862994	29683361	plus	G	alt_assembly_1	Celera	Celera	view	400
22	NT_011523.11	1042680	44150638	plus	G	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011522

dbSNP Blast Analysis
GenBank HTGS Finished:
AL021391.2 NC_000022.9

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss8019772	HapMap-CEU	European	120	IG	0.017	0.250	0.733	1.000	0.142	0.858

	HapMap-HCB	Asian	90	IG	0.044	0.222	0.733	0.317	0.156	0.844

	HapMap-JPT	Asian	88	IG		0.159	0.841	0.584	0.080	0.920

	HapMap-YRI	Sub-Saharan African	120	IG		0.083	0.917	0.752	0.042	0.958

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.185+/-0.241	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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .