Reference SNP(refSNP) Cluster Report: rs1414474

Reference SNP(refSNP) Cluster Report: rs1414474

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	88/130
Map to Genome Build:	36.3

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

HGVS Names
NM_001134734.1:c.906C>G
NM_032884.2:c.336C>G
NM_032884.3:c.336C>G
NP_001128206.1:p.Asp302Glu
NP_116273.2:p.Asp112Glu
NT_032977.8:g.4635329C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2216784 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1414474 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
ss2216784	TSC-CSHL\|TSC0610020	fwd/T	C/G	cctcttctgagcagggagctcagggagctt	tcaggacgtgcaggaggaggtcggggaggc	10/20/00	04/07/04	88	Genomic	95 %
ss5972833	SC_JCM\|NT_004511.12_1967423	rev/B	C/G	gcctccccgacctcctcctgcacgtcctga	aagctccctgagctccctgctcagaagagg	01/10/03	10/10/03	111	Genomic	unknown
ss24259767	PERLEGEN\|afd4244561	rev/B	C/G	gcctccccgacctcctcctgcacgtcctga	aagctccctgagctccctgctcagaagagg	08/10/04	09/13/04	123	Genomic	unknown
ss28497509	MGC_GENOME_DIFF\|37548184-C4601778G	rev/B	C/G	gcctccccgacctcctcctgcacgtcctga	aagctccctgagctccctgctcagaagagg	08/20/04	08/20/04	126	cDNA	unknown
ss28512226	MGC_GENOME_DIFF\|BC007637x37548184-C4601778G	rev/B	C/G	gcctccccgacctcctcctgcacgtcctga	aagctccctgagctccctgctcagaagagg	08/25/04	08/25/04	126	cDNA	unknown
ss65772122	ILLUMINA\|Human1-rs1414474	fwd/T	C/G	cctcttctgagcagggagctcagggagctt	tcaggacgtgcaggaggaggtcggggaggc	10/10/06	10/10/06	127	Genomic	unknown
ss65979185	AFFY\|SNP_A-1745541	rev/B	C/G	cccgacctcctcctgcacgtcctga	aagctccctgagctccctgctcaga	10/26/06	10/26/06	127	Genomic	unknown
ss68407725	CSHL-HAPMAP\|sanger:assay:1728046:1	fwd/	C/G	cctcttctgagcagggagctcagggagctt	tcaggacgtgcaggaggaggtcggggaggc	01/11/07	01/16/07	127	NA	unknown
ss68763207	PERLEGEN\|PGP04244561	rev/	C/G	gcctccccgacctcctcctgcacgtcctga	aagctccctgagctccctgctcagaagagg	01/30/07	08/14/07	127	Genomic	unknown
ss86272115	CORNELL\|hCV8702317	rev/	C/G	gcctccccgacctcctcctgcacgtcctga	aagctccctgagctccctgctcagaagagg	01/21/08	01/21/08	129	Genomic	unknown
ss99199432	HUMANGENOME_JCVI\|1103675065164	rev/	C/G	gcctccccgacctcctcctgcacgtcctga	aagctccctgagctccctgctcagaagagg	04/03/08	04/03/08	130	Genomic	unknown
ss110278031	1000GENOMES\|NA19240_2008_12_16_41595_chr1_34435998	rev/	C/G	gcctccccgacctcctcctgcacgtcctga	aagctccctgagctccctgctcagaagagg	12/16/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 GAGCTGCCTC TTCTGAGCAG GGAGCTCAGG GAGCTT
 S
 TCAGGACGTG CAGGAGGAGG TCGGGGAGGC AGCAGCAGAA ATGGGCTCAG CCCTGTGGGC
 TCCTTGGGTC CAGGGCCACT GAACAGGTTG TCCTGTAGGA AGTCCTTGGT GACCCTTGTC
 TTGTCCAGCA CATTCTTGTT GTCAGGGACC TTGGATGTCT CAGTGGACTT CAGTGGGAAC
 TGGGACAGAA GCTTGCTGAC TTGCAAGTTG GAGTCACCTA GGATGCGGCC CCTGTCCTCT
 GTCCCCTTGC TGCTCTTGAC CTCGGCGGCA CACAGAATGT CTGTGACAGT AGAAGTGGCA
 GAATCACAGT CCTGCCTGCT GCTGATAACG GGCATGGCCA CCTTCTGCTT CAGAAGCTTG
 TCTCCGACAA TGATGGAGGC TCTGGGGCGC TCATTACTGC CTGCCACTAG AGGAGGGGCA
 AGAATGCAGG GAGCCAGCTC TCTGGTCCCC TCGGGAGAGC TGCCGGGTAC CTCCAGCTCC
 CCAGAACTCT CTTCGACCAG GATCGAGTGC TCTTTGGTGA GG

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_004511.12 ABBA01023367 BC007637

dbSNP Blast Analysis

UniGene Cluster ID
194610

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C	C/C	C/G	G	G/G	N	HWP	C	G	N
ss2216784	AfAm	African American	40	IG			0.200		0.800		0.655	0.100	0.900

	Caucasian	European	40	IG		0.050	0.250		0.700		0.584	0.175	0.825

	Asian	Asian	40	IG			0.150		0.850		0.752	0.075	0.925

	CEPH	European	54	IG		0.111	0.259		0.630		0.150	0.241	0.759

	PDpanel	Global	48	IG			0.208		0.792		0.584	0.104	0.896

	HapMap-CEU	European	120	IG		0.050	0.233		0.717		0.251	0.167	0.833

	HapMap-HCB	Asian	90	IG			0.244		0.756		0.371	0.122	0.878

	HapMap-JPT	Asian	88	IG			0.182		0.818		0.527	0.091	0.909

	HapMap-YRI	Sub-Saharan African	118	IG			0.356		0.644		0.100	0.178	0.822

	CHMJ	Asian	74	IG	0.851			0.135		0.014		0.851	0.135	0.014

ss24259767	AFD_EUR_PANEL	European	48	IG		0.083	0.250		0.667		0.251	0.208	0.792

	AFD_AFR_PANEL	African American	46	IG			0.348		0.652		0.317	0.174	0.826

	AFD_CHN_PANEL	Asian	48	IG			0.167		0.833		0.752	0.083	0.917

ss68763207	HapMap-CEU	European	120	GF		0.050	0.250		0.700			0.175	0.825

	HapMap-HCB	Asian	90	GF		0.022	0.156		0.822			0.100	0.900

	HapMap-JPT	Asian	90	GF			0.178		0.822			0.089	0.911

	HapMap-YRI	Sub-Saharan African	120	GF		0.017	0.350		0.633			0.192	0.808

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss2216784	634	7	100	270
ss24259767	71	51	18	2
ss99199432	1		1

RefSNP Genotype Summary	Total Individual	C	C/C	C/G	G	G/G	N
rs1414474	678		58	113		272

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
548	ss2216784	G/G	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r27_ch1_CEU_affymetrix:genotype_protocol_1

Genotype data submitted for	718	samples from	678	individuals	Individual with multiple genotypes submission:	39

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 .