Reference SNP(refSNP) Cluster Report: rs34136143

Reference SNP(refSNP) Cluster Report: rs34136143

refSNP ID: rs34136143
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	126/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	G/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_018271.3:c.611C>A
NP_060741.3:p.T204N
NT_022184.14:g.67221884C>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss52062189 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs34136143 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
ss48427301	APPLERA_GI\|hCV25620385	fwd/B	G/T	ttcttgacaaaagccacatcggcaaacaca	tcttgatcggctcatcgagctcatcgctgt	09/28/05	11/03/06	126	Genomic	unknown
ss52062189	SI_EXO\|NT_022184.14_67221885	rev/T	A/C	acagcgatgagctcgatgagccgatcaaga	tgtgtttgccgatgtggcttttgtcaagaa	03/29/06	03/29/06	127	Genomic	unknown
ss68821938	PERLEGEN\|PGP17791677	rev/T	A/C	acagcgatgagctcgatgagccgatcaaga	tgtgtttgccgatgtggcttttgtcaagaa	01/30/07	03/31/08	127	Genomic	unknown

Fasta sequence (Legend)

 ACCCTCTGCT GCCGGCAGCA GGATCCCAGG ATGCTGCCCC AGGCAATGAG GGGGGAAATC
 TCCTGGGAAC TTCTGTGGGG TTTCCCATCA CCTTCAGAAC TGGGACTCCA CCTTCCTTCT
 CCTCACAGTT GCAGCCAAAG GGCAGCTAGA AGGACTGGGG CCACAGGCAT TTTTCTGGAA
 AGCCCATTTG TGCCCCGGGG ATTCCTTACC TGCAAGGTTA CCGGCAGCCC CTGTTGGCAC
 AACCACCTCC ACCAGGGGTA GGGGATGTGT GTCCAAGGAT GGCGTACACT GGAAGTAAGC
 AAAGAAGTGA TGGGCCATCT GCACCAGGAC CCGGGACCAG TTGATCGAAT TCAGGCTCAT
 CAGATTGTGC TTCTTGACAA AAGCCACATC GGCAAACACA
 K
 TCTTGATCGG CTCATCGAGC TCATCGCTGT TTCCCTCCAC TGCCAGGGGG GAGAGAAGAG
 GGCAGCTGTC AGGAGCATGT AGAACCCCCA GGAGGTCAGC ACTCACCTGC GACAGGGCCC
 TCCCAGGCTG AGCCCACCCT CCTGGGACCT TCGCGCAGCC TAGGTTTCTT TACTTTCACG
 TAGCTTGGCC TCACTATCTA GACTCAGTAT TAAGCTCCTC AAGGACAGAA ATCATGCCTC
 AGATTCTTGT GTTCCTAAAT ATCTGCCCTA GCTTAGAACA GAAAGGGTAG CCAGAACCAG
 TTCCAATGTT TCTACCATTA TCTAAAATAA GATAGCAAAT GGCAACCTTC TGGGATCCTG
 GGAGAATTTC TCTTTGTAAT CCATGCCCAC TTCCCCCACT

GeneView

GeneView via analysis of contig annotation: THNSL2 threonine synthase-like 2 (S. cerevisiae)

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_022184->NM_018271

function

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


reference	NT_022184->NM_018271->NP_060741	67221885	forward	764	missense	A	Asn [N]	2	204
					contig reference	C	Thr [T]	2	204

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs34136143 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838785.1	191976	87400819	minus	C	alt_assembly_8	HuRef	HuRef	view	400
2	NT_022184.14	67221885	88259456	minus	C	ref_assembly	reference	reference	view	400
2	NW_927808.1	827702	88307692	plus	G	alt_assembly_1	Celera	Celera	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022184.14

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_018271.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss48427301	AGI_ASP population	multiple	74	IG	0.919	0.081		1.000	0.959	0.041

ss68821938	HapMap-CEU	European	120	GF	0.967	0.033			0.983	0.017

	HapMap-HCB	Asian	90	GF	1.000				1.000

	HapMap-JPT	Asian	90	GF	1.000				1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.783	0.200	0.017		0.883	0.117

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.074+/-0.178	307	247	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 .