Reference SNP(refSNP) Cluster Report: rs733149

Reference SNP(refSNP) Cluster Report: rs733149

refSNP ID: rs733149
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:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_007101.2:c.2069+1187A>G
NT_035014.4:g.3331255T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss78929 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs733149 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
ss78929	TSC-CSHL\|TSC0023057	fwd/T	A/G	gagaggatgggaaaggagaggaggagaggc	gggaggggtgggggggagatgagtctccag	09/06/00	08/14/07	86	Genomic	95 %
ss3530675	SC_JCM\|AC000388.1_43225	fwd/T	A/G	gagaggatgggaaaggagaggaggagaggc	gggaggggtgggggggagatgagtctccag	09/24/01	10/10/03	100	Genomic	unknown
ss5802092	SC_JCM\|NT_008554.12_99790	rev/B	C/T	ctggagactcatctcccccccacccctccc	gcctctcctcctctcctttcccatcctctc	01/10/03	10/10/03	111	Genomic	unknown
ss12940757	SC_SNP\|NT_008554.15_100811	rev/B	C/T	ctggagactcatctcccccccacccctccc	gcctctcctcctctcctttcccatcctctc	10/21/03	10/31/03	119	Genomic	unknown
ss43394496	ABI\|hCV2256330	rev/B	C/T	ctggagactcatctcccccccacccctccc	gcctctcctcctctcctttcccatcctctc	07/18/05	07/18/05	126	Genomic	unknown
ss82807676	HGSV\|Cor18555_SNV_20070510.chr9_133583869	rev/B	C/T	ctggagactcatctcccccccacccctccc	gcctctcctcctctcctttcccatcctctc	11/27/07	12/03/07	130	Genomic	unknown
ss83482316	HGSV\|Cor19240_SNV_20070510.chr9_133583869	rev/B	C/T	ctggagactcatctcccccccacccctccc	gcctctcctcctctcctttcccatcctctc	11/30/07	12/05/07	130	Genomic	unknown

Fasta sequence (Legend)

 GGTCAGTGCC AGGGCTGATG GGGATGCGTC CCCCTTGTGC TCAGAAGCCT GCACACGCTC
 ACCGCCACCC TTTTTCAAGA GTTAAAAATC CTCTGTGAGA AAACGGCCTA GTCTAGGCCT
 TCCATTGGTG ACCCTCCCCC ACCAGGCTAA GGGGCCAGGA CACTCATCTC GGTGTGCTTC
 CTGCCGCCAC ATCTGCCTTG GGGCTGGACA GGGTGGCTCT GCTGGACTGG GCAGGAGGAA
 GAGGCACGAG ATGAGGGCAC TGCTTCTGGG GACATGGAGG ATATCAAAGG GGTGATCTGT
 CTCTGGAAAA TGATGGTGGC AGCTTCgggg agaggatggg aaaggagagg aggagaggc
 R
 gggaggggtg ggggggagaT GAGTCTCCAG CCTGAAGGTC GCCGAGGTGA GCACTTGACG
 TAGCAGGGCT GTGTCCTGGT GATATCCTGT CAGCCTGGGA TTCTGCCGAG ACCTCTGGCT
 GGAGTGCCCA GACCCTGCCA TGGGGTCTGC TTTCCCTGGC ACCCCACGCT GAGTCCTGGG
 CCAGTTGCTC CCCTCTCAGG CTGCAAGGGA CCGAGCTGTT GCTGTCCGTC CAAGCATATG
 CACTGTGGTG CTCAGGGGCA CACGGTAGAC GCGTG

GeneView

GeneView via analysis of contig annotation: SARDH sarcosine dehydrogenase

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_035014->NM_007101

function

HuRef

NW_001839242->NM_007101

function

Celera

NW_924573->NM_007101

function

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


reference	NT_035014->NM_007101->NP_009032	3331255	reverse	intron

HuRef	NW_001839242->NM_007101->NP_009032	100003	reverse	intron

Celera	NW_924573->NM_007101->NP_009032	20588021	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs733149 maps exactly once on NCBI human chromosome 9

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
9	NW_001839242.1	100003	106054116	minus	T	alt_assembly_8	HuRef	HuRef	view	359
9	NW_924573.1	20588021	107100190	minus	T	alt_assembly_1	Celera	Celera	view	359
9	NT_035014.4	3331255	135544136	minus	T	ref_assembly	reference	reference	view	359

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008554.12 AL365494

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL590710.14	AL954350.4

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss78929	HapMap-HCB	Asian	90	IG	0.222	0.600	0.178		0.522	0.478

	HapMap-JPT	Asian	88	IG	0.409	0.455	0.136		0.636	0.364

	HapMap-YRI	Sub-Saharan African	120	IG	0.450	0.467	0.083		0.683	0.317

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.471+/-0.117	180	150	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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .