Reference SNP(refSNP) Cluster Report: rs17176625

Reference SNP(refSNP) Cluster Report: rs17176625

refSNP ID: rs17176625
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
Map to Genome Build:	36.3

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

HGVS Names
NM_003906.3:c.3735-20A>T
NT_011515.11:g.2994256T>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss23134554 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17176625 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
ss23134554	EGP_SNPS\|MCM3AP-030229		fwd/B	A/T	gtttgaagaccctgaaaacactctgtgatg	tacattttcatgtccccaggtggagggaag	04/14/04	04/14/04	123	Genomic			unknown

Fasta sequence (Legend)

 CTCAGGCAGT CCGCCCGCCT TGGCCTCCCA AAGTGCTGGG ATTACAGGCG TGAGCCACTG
 CACCCAGCTG GGTATATGTA TCTTAAATCT GTATCCATAT TGCCAAGTCA GCCTCCAAAG
 CTCATTCAGT ATTAACTGTT AACGTTCGGT AGTTTCATTG CTCACCACAC TCATTTGATG
 TCCTTCCTTC CCCATGCCTG AGTTCTGACT GCAATGTGTT TCTCAGTTTG AAGACCCTGA
 AAACACTCTG TGATG
 W
 TACATTTTCA TGTCCCCAGG TGGAGGGAAG CTGTCACAGC CCGCAAGAAA CTGAGGCGCC
 AAATGCGGGC TTTCCCTGCT GCGCCCTGCT GCGTGGACGT GAGCGACCGG CTGAGGGCGC
 TGGCGCCCAG CGCAGAGTGC CCCATTGCTG AAGAGAACCT GGCCAGGGGC CTCCTGGACC
 TGGGCCATGC AGGGAGATTG GGCATCTCCT GCACCAGGTC AGCATCAGCT GTCGCCTGCC
 TCGTCAGGGC TCCCC

GeneView

GeneView via analysis of contig annotation: MCM3AP minichromosome maintenance complex component 3 associated protein

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_011515->NM_003906

function

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


reference	NT_011515->NM_003906->NP_003897	2994256	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17176625 maps exactly once on NCBI human chromosome 21

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
21	NW_927384.1	32274476	32789353	minus	T	alt_assembly_1	Celera	Celera	view	255
21	NW_001838717.1	167034	33060076	minus	T	alt_assembly_8	HuRef	HuRef	view	255
21	NT_011515.11	2994256	46501348	minus	T	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY590469

dbSNP Blast Analysis
GenBank HTGS Finished:
AP001469.1

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	HWP	A	T
ss23134554	PDR90	Global	174	IG	0.989	0.011	1.000	0.994	0.006

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.011+/-0.075	90	90	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .