Reference SNP(refSNP) Cluster Report: rs13374866

Reference SNP(refSNP) Cluster Report: rs13374866

refSNP ID: rs13374866
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	121/129
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_016233.2:c.347-135G>A
NT_004610.18:g.416361G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss23045343 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs13374866 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
ss23045343	WUGSC_SSAHASNP\|WUGSC_WUchr2_SNPS_200403.chr1.NT_030584.10_416361		fwd/T	A/G	caggcctctttccccagcccagagggtgca	atgccctcacctcttggatggtgtctcctt	03/22/04	03/22/04	121	Genomic			unknown

Fasta sequence (Legend)

 ATGGGGGTGG GATTTGGGGA CTGCGAGTAG CTCAGAAAGG ACACACAGCC AGGAGGCGGC
 AGAACCTGGG TTTGTGTTCA CATCTGTTTG ACACCAAAGT CCAGGCTTGC TACCCCATTC
 CAAGGAGATG AGGCAGCTTT ATATAGACAA GAATGTTCCT GGAGACCTGG GCTCAGTTCA
 GGGCATGCCT GGGACTGCAA GGGCTGCAGG GATGCAGATA GGAAGTGGTC AGGGAAGTCT
 CCCTAGAGGG GGCAGCATTT GTCCTGGGCC TTTGCTGTGA CCCTGCTTCT TGCCTCAGGC
 CTCTTTCCCC AGCCCAGAGG GTGCA
 R
 ATGCCCTCAC CTCTTGGATG GTGTCTCCTT AGAAATGACT TGCCTTTGCT CAGCCCCAGA
 CAAGCCCTGA GATCAAGGCC TGCCCTGGGC TCCTGGGAAC CTTGTAGTGA CTTACCCTCT
 GCCTCCTCTT GCAGACATCT CTCTGGATTG CGACCTGAAC TGTGAGGGAA GGCAGGACAG
 GAACTTTGTA GACAAGGTAA

GeneView

GeneView via analysis of contig annotation: PADI3 peptidyl arginine deiminase, type III

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_004610->NM_016233

function

HuRef

NW_001838572->NM_016233

function

Celera

NW_927841->NM_016233

function

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


reference	NT_004610->NM_016233->NP_057317	416361	forward	intron

HuRef	NW_001838572->NM_016233->NP_057317	393060	forward	intron

Celera	NW_927841->NM_016233->NP_057317	391158	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs13374866 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838572.1	393060	15835683	plus	G	alt_assembly_8	HuRef	HuRef	view	325
1	NW_927841.1	391158	15914715	plus	G	alt_assembly_1	Celera	Celera	view	325
1	NT_004610.18	416361	17464606	plus	G	ref_assembly	reference	reference	view	325

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030584

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL590644.14 NC_000001.9	AF188031.3 AF209070.2

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	HWP	G
ss23045343	HapMap-CEU	European	118	IG	1.000		1.000

	HapMap-HCB	Asian	88	IG	1.000		1.000

	HapMap-JPT	Asian	88	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	116	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 .