Reference SNP(refSNP) Cluster Report: rs11588976

Reference SNP(refSNP) Cluster Report: rs11588976

refSNP ID: rs11588976
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/C
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_013358.2:c.93-2074A>C
NT_004610.18:g.371053A>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16450668 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs11588976 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
ss16450668	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_030584.10_371053		fwd/T	A/C	ctcctgcctcttctgtaaaatggggattat	atctttgctttggggggttgtgatgagcat	02/17/04	03/04/04	120	Genomic			unknown

Fasta sequence (Legend)

 atgcaaagct gggggtttac ggagtgaaga aagatgatga tctggaaggg acattgagga
 gcatgaagga cccttgccca cctccaggcc caggggctgg agggagtaag ggggaagcag
 tcaccaggga gatggctgaa ggggaggcca tgcctgctat tgggggcagg cttcttttac
 agtacaagat caaggaaact gtccagggtg ggactgagga tatcgtgcag atgatggtgg
 ctgggattga aagggagttg gggaggatga ggaagggggt cagATGAGAG GATGATAGTC
 CAGGAGACTT GGGGTTTCCA TGGCAACTGA TGTAAACGAT GAGGAAGAGC AGGTAAGGTG
 CGAGGACCCC CAAAAGTGCT GTGGAATGTG GTGATTGTAA GGCCAGGAGT GGGGGATGGG
 GGAGGTGGGT CTTGCCAGCA GCCTGCAGGG GCTCCTGGGG CCCCTGCACA CTCCTGCCTC
 TTCTGTAAAA TGGGGATTAT
 M
 ATCTTTGCTT TGGGGGGTTG TGATGAGCAT TAGGGAGCGC CAAGTAGGAC TCGTGATTGT
 TGGAATTAGG ACTGTTGTCA CCGCAGTCAA TGGAGACAGT TTTTTGATGG GGCCAAGTGA
 TCATGGCAGA GGTTGTGGAG GGGGTCTGGT TTCTCCAGAG GGCTGAATAT TTGGGTGGTT
 TTTTAGGGGT CCAGGAAAGG ATGAAGGCGG GAGAATATGC AGAAGGACCC CT

GeneView

GeneView via analysis of contig annotation: PADI1 peptidyl arginine deiminase, type I

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_013358

function

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


reference	NT_004610->NM_013358->NP_037490	371053	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs11588976 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	348163	15790786	plus	A	alt_assembly_8	HuRef	HuRef	view	500
1	NW_927841.1	346213	15869770	plus	A	alt_assembly_1	Celera	Celera	view	500
1	NT_004610.18	371053	17419298	plus	A	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030584

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL590644.14	AF188031.3

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	HWP	A
ss16450668	HapMap-CEU	European	120	IG	1.000		1.000

	HapMap-HCB	Asian	90	IG	1.000		1.000

	HapMap-JPT	Asian	90	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
		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 .