Reference SNP(refSNP) Cluster Report: rs938324

Reference SNP(refSNP) Cluster Report: rs938324

refSNP ID: rs938324
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_004174.1:c.211+1245G>A
NT_006576.15:g.512982C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44636432 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs938324 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
ss1378484	TSC-CSHL\|TSC0357493	fwd/T	A/G	ccttgagaagggcccctggggcatcaggga	gtccagactcaacctgggctctgcggccgc	09/06/00	10/10/03	86	Genomic	95 %
ss6000836	SC_JCM\|NT_033317.2_1541661	rev/B	C/T	gcggccgcagagcccaggttgagtctggac	tccctgatgccccaggggcccttctcaagg	01/10/03	10/10/03	111	Genomic	unknown
ss44636432	ABI\|hCV8293135	rev/B	C/T	gcggccgcagagcccaggttgagtctggac	tccctgatgccccaggggcccttctcaagg	07/19/05	07/19/05	126	Genomic	unknown

Fasta sequence (Legend)

 CAGTGACGCC TGCCGCCTGC CCTATTTATG CCAGGGTCTC CCCTCCCCTT CAGGCCCCTT
 GTGTGTTTGC TTTCTGTCTC ATAAGGGCTC TTCTGAGCCC TCCCGCCTCC TCCCTTCTCC
 GCAGCCTCCT CCTCGCCCTG GTGTCTTTCA GCTCCCCGCC GGGCTGCCTG CTCTCCAGGC
 TCAGGCTGTC CTCCCTGGGC TTTCCACTGG GGGCTTGGGA TGCTGGCCGG GGGGGAGTCT
 CTGAGGCTGG CTGCCTCCTA CAGTTGATTT CCTTGAGAAG GGCCCCTGGG GCATCAGGGA
 R
 GTCCAGACTC AACCTGGGCT CTGCGGCCGC CCAGTCCTAA AGCTCACCCT GCTTTCCTCT
 GACGGGAGTG CCCCCCTGGT GTAAACTGAA AAGGTAATTT CTTTTTTTTT CTTTTTTTTT
 TTTTTTTGAG ATAGAATTTT GCTCTTGTTG CCCAGGCTGG AGTGCAATGA CGCGATCTCG
 GCTCACTGCA ACCTCCACAT CCTGCCTCAG CCTCCCGAGT AGCTGGGATT ACAGGCATGA
 GCCACCACGC CCAGCTAATT TGTATTTTTA GTACAGACAG GGTTTCTCCA TGTTGGTCAG

GeneView

GeneView via analysis of contig annotation: SLC9A3 solute carrier family 9 (sodium/hydrogen exchanger), member 3

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_006576->NM_004174

function

HuRef

NW_001838923->NM_004174

function

Celera

NW_922496->NM_004174

function

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


reference	NT_006576->NM_004174->NP_004165	512982	reverse	intron

HuRef	NW_001838923->NM_004174->NP_004165	1614302	forward	intron

Celera	NW_922496->NM_004174->NP_004165	507142	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs938324 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838923.2	1614302	508669	plus	G	alt_assembly_8	HuRef	HuRef	view	300
5	NT_006576.15	512982	575982	minus	C	ref_assembly	reference	reference	view	300
5	NW_922496.1	507142	619214	minus	C	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033317.2

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	HWP	A	G
ss1378484	CEPH		184	AF				1.000

ss44636432	HapMap-CEU	European	106	IG	1.000			1.000

	HapMap-HCB	Asian	74	IG	1.000			1.000

	HapMap-JPT	Asian	82	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	104	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
		270	210	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 .