Reference SNP(refSNP) Cluster Report: rs1141534

Reference SNP(refSNP) Cluster Report: rs1141534

refSNP ID: rs1141534
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:	G/T
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_004368.2:c.384G>T
NM_201277.1:c.384G>T
NP_004359.1:p.A128A
NP_958434.1:p.A128A
NT_011255.14:g.972688G>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss69378195 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1141534 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
ss1552880	LEE\|1346851	fwd/B	G/T	gcaggtgcaggtgtctcttctcgccctggc	gggaaggccaagactaaggggctgcagagc	09/13/00	10/10/03	86	cDNA	unknown
ss2424083	HGBASE\|SNP000011430	fwd/B	G/T	tgcaggtgtctcttctcgccctggc	gggaaggccaagactaaggggctgc	11/07/00	10/10/03	102	cDNA	unknown
ss3251110	YUSUKE\|IMS-JST061195	rev/T	A/C	tggctgcccctctctgggcctcaccttccc	gccagggcgagaagagacacctgcacctgc	09/05/01	10/10/03	105	Genomic	unknown
ss24813122	SEQUENOM\|sqnm204024	fwd/B	G/T	gcaggtgcaggtgtctcttctcgccctggc	gggaaggccaagactaaggggctgcagagc	06/18/04	06/18/04	130	cDNA	unknown
ss48419389	APPLERA_GI\|hCV9611818	rev/T	A/C	tggctgcccctctctgggcctcaccttccc	gccagggcgagaagagacacctgcacctgc	09/28/05	11/03/06	126	Genomic	unknown
ss69378195	SI_EXO\|NT_011255.14_972689	fwd/B	G/T	gcaggtgcaggtgtctcttctcgccctggc	gggaaggtgaggcccagagaggggcagcca	04/12/07	04/12/07	127	Genomic	unknown

Fasta sequence (Legend)

 CCCAGGAAGG CGTGAGCTTG GCTGAGATCA GCATCGGGTC TTCACGGTTC CTCGCTGCTC
 ACAGAGGTTT CTGTTTCCCC CGCCCCATGT TGTGCCCTCC AGACTCATGA ACAAGCTACA
 GCCGGGCTCC GTCCCCAAGA TCAACCGCTC CATGCAGAAC TGGCACCAGG TGAGGGGCTG
 GTGGAGCGGA GCAGGGATGG TGCTGGGGGC CCATCTAACA GGTGGGGAGA CTGAGGCCCA
 CTCACTGTCC CTCTCCTGCC TCTTCCCAGC TAGAAAACCT GTCCAACTTC ATCAAGGCCA
 TGGTCAGCTA CGGCATGAAC CCTGTGGACC TGTTCGAGGC CAACGACCTG TTTGAGAGTG
 GGAACATGAC GCAGGTGCAG GTGTCTCTTC TCGCCCTGGC
 K
 GGGAAGGTGA GGCCCAGAGA GGGGCAGCCA CCTGCCCAGA GTCACACAGC GAGGTGGATG
 TAGCTGCTGC ATTCACTCGT TTGCAAATTT CTGTTTGTTT ATTTTTGAGT CGGAGTCTCA
 CTCTGTCACT CAGGCTGGAG TGCAATGGCG TGATCTCAGC TCACTGCAAC CTCCAACTCC
 CAGGTTCAAG CGATTCTTCT GCCTCAGTCT CCCGAGTAGC TGGGATTACA GGCACCTGCC
 ACCACGCCTG GCTAATTTTT GTATTTTTAG TGGAGACTGG GTTTCACCAT GCTGGCCAGG
 CTGGTCTTGA ACTCTTGACT TCAGGTGATC CGCCCGCCTC GGCCTCCCCA AGTGCTGGGA
 TTACAGGCAT GAGCCCCTGT GCCCGGCCTC GTTTACAAAT

GeneView

GeneView via analysis of contig annotation: CNN2 calponin 2

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_011255->NM_004368

function

reference

NT_011255->NM_201277

function

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


reference	NT_011255->NM_004368->NP_004359	972689	forward	747	synonymous	T	Ala [A]	3	128
					contig reference	G	Ala [A]	3	128

reference	NT_011255->NM_201277->NP_958434	972689	forward	747	synonymous	T	Ala [A]	3	128
					contig reference	G	Ala [A]	3	128

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1141534 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838476.1	795178	805979	plus	G	alt_assembly_8	HuRef	HuRef	view	400
19	NW_927173.1	223753	965029	plus	G	alt_assembly_1	Celera	Celera	view	400
19	NT_011255.14	972689	983689	plus	G	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm204024	NT_011255.14 Hs.169718

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_004368.2 NM_201277.1

UniGene Cluster ID
169718

3D structure mapping
NP_004359 NP_958434

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss48419389	AGI_ASP population	multiple	72	IG	0.722	0.222	0.056	0.251	0.833	0.167

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.278+/-0.248	39	39	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .