Reference SNP(refSNP) Cluster Report: rs12349

Reference SNP(refSNP) Cluster Report: rs12349

refSNP ID: rs12349
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/129
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_022482.3:c.*1402A>G
NT_011387.8:g.23292480A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8360425 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12349 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
ss14621	CGAP-GAI\|59097	rev/B	C/T	atttctggcatagtgcagctacatgttcat	ctggaacttaaagtaccttcctcttagaaa	08/23/99	04/07/04	52	cDNA	99 %
ss1517966	LEE\|235211	fwd/T	A/G	tttctaagaggaaggtactttaagttccag	atgaacatgtagctgcactatgccagaaat	09/13/00	10/10/03	86	cDNA	unknown
ss4410294	LEE\|e235211	fwd/T	A/G	tttctaagaggaaggtactttaagttccag	atgaacatgtagctgcactatgccagaaat	04/26/02	10/10/03	106	cDNA	unknown
ss8360425	SC_SNP\|NT_011387.8_23292480	fwd/T	A/G	tttctaagaggaaggtactttaagttccag	atgaacatgtagctgcactatgccagaaat	04/17/03	05/16/04	114	Genomic	unknown
ss24690505	PERLEGEN\|afd0421440	fwd/T	A/G	tttctaagaggaaggtactttaagttccag	atgaacatgtagctgcactatgccagaaat	08/10/04	09/13/04	123	Genomic	unknown
ss69380366	SI_EXO\|NT_011387.8_23292480	fwd/T	A/G	tttctaagaggaaggtactttaagttccag	atgaacatgtagctgcactatgccagaaat	04/12/07	04/12/07	127	Genomic	unknown
ss77540806	HGSV\|Cor12156_SNV_20070510.chr20_23300480	fwd/T	A/G	tttctaagaggaaggtactttaagttccag	atgaacatgtagctgcactatgccagaaat	10/09/07	10/13/07	129	Genomic	unknown
ss83176062	HGSV\|Cor18555_SNV_20070510.chr20_23300480	fwd/T	A/G	tttctaagaggaaggtactttaagttccag	atgaacatgtagctgcactatgccagaaat	11/27/07	12/04/07	130	Genomic	unknown
ss83477896	HGSV\|Cor18956_SNV_20070510.chr20_23300480	fwd/T	A/G	tttctaagaggaaggtactttaagttccag	atgaacatgtagctgcactatgccagaaat	11/30/07	12/05/07	130	Genomic	unknown

Fasta sequence (Legend)

 CCTTGGGAGC ATGTGAGAAC ATAGCAGTAG GGACCAAAAG TCTCAGCACA CTTACCTCCG
 ATTATGCCTT AAAGAGTTGA TTGTGAAGAA CCAGTAACTT TGTCCCAAAT GCTTCTTTGG
 CTGTTTCATG CAGGACTTAA TTATTGCTTT TAAAAATTCA CAATGAAAAG ACGATTCTGC
 TGTATTTGTT AAACGTTGAC ATTTGGTTCT AGGGCCTTGA GTATGTGCCA CGTGCTTGTG
 AAATGCTATG ATTCACATGT AACATTTAAA CATTAATTTA AAAAGGGAAC CTTGGAGAAT
 TCTTTTGTTC ACTAGTTCCT TTTTTCTCTA CATTTTTAAT TTATTAAACT TGCTGTGAAA
 ACACTTTGAT TTTCTAAGAG GAAGGTACTT TAAGTTCCAG
 R
 ATGAACATGT AGCTGCACTA TGCCAGAAAT TAATGAGGGA AGACTTTCTT CCTAAGTGCT
 TATGTTTTAA CTTATGTTAG TGAAACCACT ACAAGGTGTT TCAGGCGCTG ATAACATGCT
 TCACACCTGC CCTTGGAGGT CACAGTACTA ATTTACTTCA AATTTAGTTA TGACAGTGTC
 ACTGTATCCT AGTTATGTTT ACAGCACAAA TAAATAATGA CTGTCATACA TCCAGAGGAG
 ACCGAACCTG CCCAGCTGAT GTACTGTTTT ATGGAATAAA GTCACTTGAT CAGAAGGAAT
 TGAAACAATA GATCATTTTG TTACCTACTG GAGGGATTTT TGTCTTGAAT TTGTTTCCTT
 AGAAATTCTA CAAAAAAATG TTGTTAATAA ATGTCTGCTT

GeneView

GeneView via analysis of contig annotation: GZF1 GDNF-inducible zinc finger protein 1

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_011387->NM_022482

function

HuRef

NW_001838653->NM_022482

function

Celera

NW_927317->NM_022482

function

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


reference	NT_011387->NM_022482->	23292480	forward	3538	3' UTR

HuRef	NW_001838653->NM_022482->	898549	forward	3539	3' UTR

Celera	NW_927317->NM_022482->	23283029	forward	3538	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12349 maps exactly once on NCBI human chromosome 20

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
20	NT_011387.8	23292480	23300480	plus	A	ref_assembly	reference	reference	view	400
20	NW_001838653.1	898549	23314120	plus	A	alt_assembly_8	HuRef	HuRef	view	400
20	NW_927317.1	23283029	23425853	plus	A	alt_assembly_1	Celera	Celera	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011387.8 AI023363 Hs.28921

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank mRNA:
NM_022482.3	AL096677.21 NC_000020.9	AK025447.1

UniGene Cluster ID
28921

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss14621	POOLED_CEPH		188	AF					0.477	0.523

ss24690505	AFD_EUR_PANEL	European	48	IG	0.250	0.542	0.208	0.752	0.521	0.479

	AFD_AFR_PANEL	African American	46	IG		0.261	0.739	0.479	0.130	0.870

	AFD_CHN_PANEL	Asian	48	IG		0.167	0.833	0.752	0.083	0.917

ss8360425	CEPH		184	AF					0.480	0.520

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.371+/-0.219	71	50	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

UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .