Reference SNP(refSNP) Cluster Report: rs1748013

Reference SNP(refSNP) Cluster Report: rs1748013

refSNP ID: rs1748013
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	89/129
Map to Genome Build:	36.3

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

HGVS Names
NM_012387.1:c.1156-835A>T
NT_004610.18:g.504535A>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2595318 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1748013 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
ss2595318	SC_JCM\|AL138798.4_24601		fwd/T	A/T	ataaaccaggataatcaccccatcacaaga	ccctaatataattacattcagcaaagtccc	11/03/00	10/25/06	89	Genomic			unknown
ss13032034	SC_SNP\|NT_030584.9_504535		rev/B	A/T	gggactttgctgaatgtaattatattaggg	tcttgtgatggggtgattatcctggtttat	10/22/03	10/31/03	119	Genomic			unknown

Fasta sequence (Legend)

 AGTCCAGGGA TGGCAGAGCT GGTTCCTCCT GGAGGCCCTG AGGAAAGAAT CTATTATATT
 TCCGTGTCTT TTTCAGCTTC TAATAGCCGc cttggctggc agccccttct tccaccttca
 aagatctcca gtctctgctt ccatcatcac aGGCCCTCCC GCATTccagg ataaaccagg
 ataatcaccc catcacaaga
 W
 ccctaatata attacattca gcaaagtccc ttttaccata taaggaaaca tcaggttcgg
 ggggactagg atgtagaggg gccattattc agtccaccgc CCATCTCCCC TGCCTCCCAG
 GAGAGGGTAC ATCTAGCCTT CTACACATAG ATGGTCCATT CCCTGAGGCT TCATGGGGGC
 CATGAACTCC CTGAGAGTAG

GeneView

GeneView via analysis of contig annotation: PADI4 peptidyl arginine deiminase, type IV

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_012387

function

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


reference	NT_004610->NM_012387->NP_036519	504535	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1748013 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	483862	15926485	minus	A	alt_assembly_8	HuRef	HuRef	view	200
1	NW_927841.1	482011	16005568	minus	A	alt_assembly_1	Celera	Celera	view	200
1	NT_004610.18	504535	17552780	minus	A	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030584 AC004824

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/T	T/T	HWP	A	T
ss2595318	HapMap-CEU	European	118	IG	0.085	0.915	0.752	0.042	0.958

	HapMap-HCB	Asian	84	IG		1.000			1.000

	HapMap-JPT	Asian	86	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.024+/-0.107	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 .