Reference SNP(refSNP) Cluster Report: rs1758567

Reference SNP(refSNP) Cluster Report: rs1758567

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	89/130
Map to Genome Build:	36.3

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

HGVS Names
NM_024013.1:c.29T>C
NP_076918.1:p.Val10Ala
NT_008413.17:g.21430535T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76899064 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1758567 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
ss2611175	SC_JCM\|AL353732.11_115926	fwd/B	C/T	cgatggcctcgccctttgctttactgatgg	cctggtggtgctcagctgcaagtcaagctg	11/03/00	05/16/04	89	Genomic	unknown
ss3173356	WIAF-CSNP\|WIAF-13928	fwd/B	C/T	ygatggcctcgccctttgctttactgatgg	cctggtggtgctcagctgcaagtcaagctg	06/19/01	04/07/04	98	cDNA	unknown
ss3922004	SC_JCM\|AL162420.8_133147	rev/T	A/G	cagcttgacttgcagctgagcaccaccagg	ccatcagtaaagcaaagggcgaggccatca	09/25/01	10/10/03	103	Genomic	unknown
ss35085946	JDRF_WT_DIL\|DIL9948	fwd/B	C/T	cgatggcctcgccctttgctttactgatgg	cctggtggtgctcagctgcaagtcaagctg	03/14/05	03/25/05	125	Genomic	unknown
ss48397521	EGP_SNPS\|IFNA1-002085	fwd/B	C/T	cgatggcctcgccctttgctttactgatgg	cctggtggtgctcagctgcaagtcaagctg	08/30/05	11/03/06	126	Genomic	unknown
ss76899064	SI_EXO\|NT_008413.17_21430535	fwd/B	C/T	cgatggcctcgccctttgctttactgatgg	cctggtggtgctcagctgcaagtcaagctg	09/20/07	09/20/07	129	Genomic	unknown
ss85603925	HGSV\|Cor19129_SNV_20070510.chr9_21430535	fwd/B	C/T	cgatggcctcgccctttgctttactgatgg	cctggtggtgctcagctgcaagtcaagctg	12/06/07	12/09/07	130	Genomic	unknown

Fasta sequence (Legend)

 ATTAAACTTT GTACTTTTTG ATTATAGAGA TATACATATA GTATATAAAT AGATACATAT
 TGTATCTGTG TTATTAAATT TTCACGGTGG GTTCAATTAG GAAAAAGATA TCTAAAAAGT
 CTCTGGGAAC AAGATGGGGA AGACAATAAT GAAAAACAAA ACATTTGAGA AACACGGCTC
 TAAACTCATG TAAAGAGTGC ATGAAGGAAA GCAAAAACAG AAATGGAAAG TGGCCCAGAA
 GCATTAAGAA AGTGGAAATC AGTATGTTCC CTATTTAAGG CATTTGCAGG AAGCAAGGCC
 TTCAGAGAAC CTAGAGCCCA AGGTTCAGAG TCACCCATCT CAGCAAGCCC AGAAGTATCT
 GCAATATCTA CGATGGCCTC GCCCTTTGCT TTACTGATGG
 Y
 CCTGGTGGTG CTCAGCTGCA AGTCAAGCTG CTCTCTGGGC TGTGATCTCC CTGAGACCCA
 CAGCCTGGAT AACAGGAGGA CCTTGATGCT CCTGGCACAA ATGAGCAGAA TCTCTCCTTC
 CTCCTGTCTG ATGGACAGAC ATGACTTTGG ATTTCCCCAG GAGGAGTTTG ATGGCAACCA
 GTTCCAGAAG GCTCCAGCCA TCTCTGTCCT CCATGAGCTG ATCCAGCAGA TCTTCAACCT
 CTTTACCACA AAAGATTCAT CTGCTGCTTG GGATGAGGAC CTCCTAGACA AATTCTGCAC
 CGAACTCTAC CAGCAGCTGA ATGACTTGGA AGCCTGTGTG ATGCAGGAGG AGAGGGTGGG
 AGAAACTCCC CTGATGAATG CGGACTCCAT CTTGGCTGTG

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_008413.17 AL162420 AL353732

dbSNP Blast Analysis

UniGene Cluster ID
37026

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss2611175	CEPH		184	AF					0.110	0.890

ss3173356	WIAF-CSNP-MITOGPOP5	multiple	58	IG	0.517	0.172	0.310	0.001	0.603	0.397

ss48397521	HapMap-CEU	European	120	IG		0.183	0.817	0.439	0.092	0.908

	HapMap-HCB	Asian	84	IG		0.024	0.976	1.000	0.012	0.988

	HapMap-JPT	Asian	86	IG			1.000			1.000

	EGP_YORUB-PANEL	Sub-Saharan African	24	AF		0.333	0.667	0.527	0.167	0.833

	EGP_HISP-PANEL	Hispanic	44	AF		0.136	0.864	0.752	0.068	0.932

	EGP_CEPH-PANEL	European	44	AF		0.318	0.682	0.403	0.159	0.841

	EGP_AD-PANEL	African American	30	AF		0.333	0.667	0.479	0.167	0.833

	EGP_ASIAN-PANEL	Asian	48	AF		0.042	0.958	1.000	0.021	0.979

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss3173356	27	15	4	8
ss48397521	94		19	75
ss76899064	347		16	157

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs1758567	423	15	32	203

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
467	ss3173356	C/T	WIAF-CSNP	WIAF-CSNP-MITOGPOP5	CL6		06.18.01-a
467	ss76899064	T/T	CSHL-HAPMAP	HapMap-CEU	NA12006	CEPH1420.12	r27_ch9_CEU_illumina:golden_gate_1.0.0
536	ss3173356	T/T	WIAF-CSNP	WIAF-CSNP-MITOGPOP5	CL8		06.18.01-a
536	ss48397521	C/T	EGP_SNPS	EGP_CEPH-PANEL	E111	NA12751	IFNA1-EGP_CEPH-083005	695968
536	ss76899064	C/T	CSHL-HAPMAP	HapMap-CEU	NA12751	CEPH1444.14	r27_ch9_CEU_illumina:golden_gate_1.0.0

Genotype data submitted for	473	samples from	423	individuals	Individual with multiple genotypes submission:	49

Validation Summary:

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

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Revised: May 25, 2006 1:38 PM .