Reference SNP(refSNP) Cluster Report: rs28562308

Reference SNP(refSNP) Cluster Report: rs28562308

refSNP ID: rs28562308
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	125/129
Map to Genome Build:	36.3

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

HGVS Names
NM_003648.2:c.2562+390C>T
NM_152879.2:c.2694+390C>T
NT_005120.15:g.300187C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss35298854 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs28562308 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
ss35298854	SSAHASNP\|TA-079.chr2_234149433	fwd/B	C/T	gcccaccaccattcccagctaatttttgta	ttcaccatgttggccaggctggtctcgaac	03/11/05		125	Genomic	unknown
ss80622109	HGSV\|Cor18507_SNV_20070510.chr2_234149433	fwd/B	C/T	gcccaccaccattcccagctaatttttgta	ttcaccatgttggccaggctggtctcgaac	11/23/07	11/26/07	130	Genomic	unknown
ss110962609	1000GENOMES\|CEU.trio.12.15.2008_607848_chr2_234032172	fwd/B	C/T	gcccaccaccattcccagctaatttttgta	ttcaccatgttggccaggctggtctcgaac	12/15/08	12/17/08	130	Genomic	unknown
ss111822717	1000GENOMES\|NA19240_2008_12_16_543591_chr2_234032172	fwd/B	C/T	gcccaccaccattcccagctaatttttgta	ttcaccatgttggccaggctggtctcgaac	12/16/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 GCCATGGTCC TGGGGTGTCT GGCCGAGTCC CCAGCCCGGA GTGTGCTAAA TTCTGGGGCA
 GTGCATGGAG CCTGGGAGGG TGGGCGCTTT CCAGGGCCAT GTGGCTGCCT CATGTCCTGT
 CCTGGACAGC TCGTGGCCCC ACTTCCTGGG CCAGAGCCCT TTCCTTGTGC TATGCTTGAC
 AGTTAAATTC TCAAGATAAC TCTTTTTAAT TTTTTTTTTT TTTTTTGAGA CAGAGTCTTG
 CTCTGTTGCC CAGGCTGGAG TGCAGTGGTG CAATCTCGGC TTGCTGCAAC CTCCACCTCC
 CTGGTTCAAG TGATTCTCCC GCCTCAGCCT TCCGAGTAGC TGGGACTACA AGTGCCCACC
 ACCATTCCCA GCTAATTTTT GTA
 Y
 TTCACCATGT TGGCCAGGCT GGTCTCGAAC TCCTGACCTC AAATGATCCA CCCACCTTGG
 CCTCCCAAAG TGTTGGGATT ACAGGTGTGA GCCACTGCAC CCGGCCAAGA TAACTCTTTC
 AAAATGTGTA TCCTGCTTGA ACCACAGCCT TGCCTGTCCC CTCTGAGGTG GGATGAGATA
 GAGCAGACCC AGGCTGGACT CTGCCCGTGT CTGCAGCTGT CAAAGCCGCA GTGGGGACGG
 AGCCCATGGC TCTGATGTGG GGTGTGGGAG GATTTCCAGC TGGGGCCCTC GATCATGGTT
 CTGAGG

GeneView

GeneView via analysis of contig annotation: DGKD diacylglycerol kinase, delta 130kDa

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_005120->NM_003648

function

reference

NT_005120->NM_152879

function

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


reference	NT_005120->NM_003648->NP_003639	300187	forward	intron

reference	NT_005120->NM_152879->NP_690618	300187	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs28562308 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_001838868.1	313667	226168125	plus	C	alt_assembly_8	HuRef	HuRef	view	383
2	NW_921618.1	39003234	228088704	plus	C	alt_assembly_1	Celera	Celera	view	383
2	NT_005120.15	300187	234032172	plus	C	ref_assembly	reference	reference	view	383

NCBI Resource Links

Submitter-Referenced

dbSNP Blast Analysis

Population Diversity

There is no frequency data.

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 .