Reference SNP(refSNP) Cluster Report: rs17244979

Reference SNP(refSNP) Cluster Report: rs17244979

refSNP ID: rs17244979
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/G
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_001012339.2:c.1407C>G
NM_194283.3:c.1542C>G
NP_001012339.2:p.V469V
NP_919259.3:p.V514V
NT_006576.15:g.34926835C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss24425254 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17244979 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
ss24425254	PERLEGEN\|afd3693650		fwd/B	C/G	aaagaaaaccaaagatatgaaaaaacctgt	agagtacctgctgaaccacaaacaatggta	08/10/04	09/13/04	123	Genomic			unknown

Fasta sequence (Legend)

 GGTTAAAAGG AGTATGTTAT TTTTGGATTA TGCTGAATTA TTTATTTTCC AGTGTTCCTA
 AACCCAAAGG AAAGAAAACC AAAGATAT
 GAAAAAACCT GT
 S
 AGAGTACCTG CT
 GAACCACAAA CAATGGTAGG TCAAAATCAT ATTCATATCT CTTTAGCATA TCTTGCTGTT
 TAAGCAGTAT AATGATCTAA AGATGGAA

GeneView

GeneView via analysis of contig annotation: DNAJC21 DnaJ (Hsp40) homolog, subfamily C, member 21

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_001012339

function

reference

NT_006576->NM_194283

function

HuRef

NW_001838932->NM_001012339

function

HuRef

NW_001838932->NM_194283

function

Celera

NW_922596->NM_001012339

function

Celera

NW_922596->NM_194283

function

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


reference	NT_006576->NM_001012339->NP_001012339	34926836	forward	1634	synonymous	G	Val [V]	3	469
					contig reference	C	Val [V]	3	469

reference	NT_006576->NM_194283->NP_919259	34926836	forward	1769	synonymous	G	Val [V]	3	514
					contig reference	C	Val [V]	3	514

HuRef	NW_001838932->NM_001012339->NP_001012339	754456	reverse	1632	missense	G	Glu [E]	1	469
					contig reference	C	Gln [Q]	1	469

HuRef	NW_001838932->NM_194283->NP_919259	754456	reverse	1767	missense	G	Glu [E]	1	514
					contig reference	C	Gln [Q]	1	514

Celera	NW_922596->NM_001012339->NP_001012339	546827	forward	1634	synonymous	G	Val [V]	3	469
					contig reference	C	Val [V]	3	469

Celera	NW_922596->NM_194283->NP_919259	546827	forward	1769	synonymous	G	Val [V]	3	514
					contig reference	C	Val [V]	3	514

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17244979 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_922596.1	546827	34836313	plus	C	alt_assembly_1	Celera	Celera	view	100
5	NW_001838932.2	754456	34902834	minus	G	alt_assembly_8	HuRef	HuRef	view	100
5	NT_006576.15	34926836	34989836	plus	C	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000005.5

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC008795.7 NC_000005.8	AC011145.3

UniGene Cluster ID
131887

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss24425254	AFD_EUR_PANEL	European	48	IG	0.708	0.292		0.439	0.854	0.146

	AFD_AFR_PANEL	African American	46	IG	1.000				1.000

	AFD_CHN_PANEL	Asian	48	IG	0.875	0.125		0.752	0.938	0.062

	HapMap-CEU	European	118	IG	0.831	0.153	0.017	0.479	0.907	0.093

	HapMap-HCB	Asian	90	IG	0.889	0.111		0.752	0.944	0.056

	HapMap-JPT	Asian	90	IG	0.956	0.044			0.978	0.022

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

	CHMJ	Asian	74	IG					0.946	0.054

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.095+/-0.196	332	260	9	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 .