Reference SNP(refSNP) Cluster Report: rs12039455

Reference SNP(refSNP) Cluster Report: rs12039455

refSNP ID: rs12039455
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

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

HGVS Names
NM_012387.1:c.527-402A>G
NT_004610.18:g.490123A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss18103924 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12039455 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
ss18103924	SC_SNP\|SC-CHR1_NA11321-200402.chr1.NT_030584.10_490123		fwd/T	A/G	ttggttcacaaaccccacttcttgctcagg	ccagcacagaaacctttcactcgttcattg	02/20/04	03/04/04	120	Genomic			unknown

Fasta sequence (Legend)

 TGGCCTGGCC CGATGCCAGG GGACAGCCTC TGTACAGTGC CTGACATGCG GTAATAATCA
 CAACAGCTGT CCTTTGtggg cactcccggg gtgccaagag ctggtataag cactgtgtat
 cacctgactt tatcttcaca accattctac ggtgggtaca actcttgccc ctgtcttagt
 gatgaggaaa cagaggcaga gaaagctgaa atccgtttcc taagcccacc cagATCCCAG
 ATTCAAACCA AATTGACCGC AAAGCCTTTA AGCCCTTGGC TATCAGTCAG TCCCTTGGGA
 ACCATCTCTT CACTCTCCCC ACCCTCTACC CCTTCTTGGC TATTGTTCAA GTTGGTTCAC
 AAACCCCACT TCTTGCTCAG G
 R
 CCAGCACAGA AACCTTTCAC TCGTTCATTG CACAAATCTC AGCCGAGCGC CTGCCGCCTG
 CTGGTCATTG TTCTAGGGAG TTCTCGGCTT TCTAGGTTCA AGATTCAGGG AACGTTGCAA
 GGAGCAAAAT ATTAATAAAT GTGGTCCCCG CTTTGCTGAG GTTACATCCC CAGCTCATCC
 TAGTGGGAGG AGACCAAAAC CTTAATGAGC TCTCATTCCA AAATGAAAAC CATCATTTAA
 ATACTCAAAA TAGCATAAA

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	490123	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12039455 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	469423	15912046	plus	A	alt_assembly_8	HuRef	HuRef	view	381
1	NW_927841.1	467605	15991162	plus	A	alt_assembly_1	Celera	Celera	view	381
1	NT_004610.18	490123	17538368	plus	A	ref_assembly	reference	reference	view	381

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030584

dbSNP Blast Analysis
GenBank HTGS Draft:
AF209070.2

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	HWP	A
ss18103924	HapMap-CEU	European	118	IG	1.000		1.000

	HapMap-HCB	Asian	86	IG	1.000		1.000

	HapMap-JPT	Asian	90	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	114	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 .