Reference SNP(refSNP) Cluster Report: rs2240552

Reference SNP(refSNP) Cluster Report: rs2240552

refSNP ID: rs2240552
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	98/129
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_015148.2:c.876+69C>T
NT_005416.12:g.1251903G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44151472 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2240552 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Success Rate
ss3196230	YUSUKE\|IMS-JST012152	fwd/T	A/G	cacccttgccttcagaaacccttggtctgc	tctccagttatggattcagagctaagaact	08/07/01	10/10/03	98	Genomic	unknown
ss20094679	CSHL-HAPMAP\|CSHL-HuFF-200402.chr2.NT_005416.11_1251903	fwd/T	A/G	cacccttgccttcagaaacccttggtctgc	tctccagttatggattcagagctaagaact	02/21/04	03/04/04	120	Genomic	unknown
ss44151472	ABI\|hCV16177131	fwd/T	A/G	cacccttgccttcagaaacccttggtctgc	tctccagttatggattcagagctaagaact	07/18/05	11/03/06	126	Genomic	unknown
ss46564149	IMCJ-GDT\|IMCJ-PASK_25-CT	rev/B	C/T	agttcttagctctgaatccataactggaga	gcagaccaagggtttctgaaggcaagggtg	08/02/05	08/02/05	126	Genomic	unknown
ss75112693	ILLUMINA\|ILMN_Human_1M_rs2240552	fwd/T	A/G	cacccttgccttcagaaacccttggtctgc	tctccagttatggattcagagctaagaact	08/28/07	08/29/07	129	Genomic	unknown
ss76524324	AFFY\|AFFY_6_1M_SNP_A-8385552	rev/B	C/T	aatccataactggaga	gcagaccaagggtttc	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 GCCACGCCAC TGGCAACTGT GCCATCCTTG ATCTGGCACC AGGATACTGG CCCCACAGGC
 AGCACTACAC CAGCTGCGCA GCTGTGGATG TTACCTCCCA CCCCTCAGCC TTGGGCAGCG
 TCCCAGCATC CACCTCTGTG GGTGGCCCAG CTCCTGGGAG AAGACTCAGG GGACAAGAGT
 GGTCAGCTGG GAGACCACAT AGGCTCCGGC CCTTGGTCAA GGCCTCAGCG CACAGGAAGC
 TCAAAACTGA GCATGTCCCA CCCCTAAGGC CACCCTTGCC TTCAGAAACC CTTGGTCTGC
 R
 TCTCCAGTTA TGGATTCAGA GCTAAGAACT CCACCCCATC ACACAGTGCG GGAGGTCAGG
 AGCCCTACCT TTGGGATGTG CTGGCCAGAA GGAGGGAGCT GCACAGAAGG GATCAGGTCT
 GTGATATGCT GCCCAGCCAC GTCCTCCCCA GACACGTACC CGTGAAGATG AGCAAAGAGA
 CTGTCACATG ACGTGACGGT GCCCTGGAGG AAAAGCCCCG TGCTTATCAT AAAAGCTTCT
 TGTGCTCCAG CTGTAAATTT AACTAAGCTT CAATATGTTC AAGCCAAAAG CAAGACCCCA

GeneView

GeneView via analysis of contig annotation: PASK PAS domain containing serine/threonine kinase

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_005416->NM_015148

function

HuRef

NW_001838874->NM_015148

function

Celera

NW_921618->NM_015148

function

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


reference	NT_005416->NM_015148->NP_055963	1251903	reverse	intron

HuRef	NW_001838874->NM_015148->NP_055963	321007	reverse	intron

Celera	NW_921618->NM_015148->NP_055963	46661553	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2240552 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NW_001838874.1	321007	233833746	plus	G	alt_assembly_8	HuRef	HuRef	view	300
2	NW_921618.1	46661553	235747023	plus	G	alt_assembly_1	Celera	Celera	view	300
2	NT_005416.12	1251903	241725972	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_005416

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC005237.2 NC_000002.10	AC016366.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss3196230	JBIC-allele		1094	AF					0.299	0.701

ss44151472	HapMap-CEU	European	120	IG			1.000			1.000

	HapMap-HCB	Asian	90	IG	0.044	0.467	0.489	0.294	0.278	0.722

	HapMap-JPT	Asian	88	IG	0.023	0.477	0.500	0.150	0.261	0.739

	HapMap-YRI	Sub-Saharan African	120	IG			1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.203+/-0.246	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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .