Reference SNP(refSNP) Cluster Report: rs310622

Reference SNP(refSNP) Cluster Report: rs310622

refSNP ID: rs310622
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NT_011333.5:g.887945G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss8378062 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs310622 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
ss398993	KWOK\|OVLP-000621-240447	rev/T	A/G	cggggccgagggaggtgtggggaggattct	cgctggggggaggaggagagggaggacgcc	06/30/00	10/10/03	79	Genomic	99 %
ss399955	KWOK\|OVLP-000621-243006	rev/T	A/G	cggggccgagggaggtgtggggaggattct	cgctggggggaggaggagagggaggacgcc	06/30/00	10/10/03	85	Genomic	99 %
ss596698	SC_JCM\|AL121907.23_8144	rev/T	A/G	cggggccgagggaggtgtggggaggattct	cgctggggggaggaggagagggaggacgcc	07/12/00	10/10/03	85	Genomic	unknown
ss2585559	SC_JCM\|AL121829.29_64230	fwd/B	C/T	ggcgtcctccctctcctcctccccccagcg	agaatcctccccacacctccctcggccccg	11/03/00	10/10/03	89	Genomic	unknown
ss8378062	SC_SNP\|NT_011333.5_887945	rev/T	A/G	cggggccgagggaggtgtggggaggattct	cgctggggggaggaggagagggaggacgcc	04/17/03	10/10/03	114	Genomic	unknown
ss74988398	ILLUMINA\|ILMN_Human_1M_rs310622	fwd/B	C/T	ggcgtcctccctctcctcctccccccagcg	agaatcctccccacacctccctcggccccg	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 GCCCTCCGGC CCGGCCTCCA GGGACTTCGC AGCCAGAGGA ACCTGGATCT CTCCCGAGTC
 CCCCTCACAG CTCTGGCAGC TCCGGAACCT GCACCCCGGT TGCCCAGCCC CAGGACGCGC
 CTGCTGCCCG CAGGGGGCGG TGAAAGGGTG GGCGGATGGC GGGGCAGTGG GAGGCGGGGC
 CCAGTCGGAG AGCGGGGCGG ATTTGGGCGG GTGAGGTGAG TCTCCAGTCG CCGGAGGCAG
 AGGCTGGGCC CCACTGCTCG GAGACCCCAT GTTTGGGGAG CCCAGAGCGT TCCCGGCAGG
 GCCCTGGGGC CCGGGGGACG GCCCGCCATG CCAATCAGGA GGGGGCGCGT TTTCCCTTCC
 CAGGCAGAAA GGCGTCCTCC CTCTCCTCCT CCCCCCAGCG
 Y
 AGAATCCTCC CCACACCTCC CTCGGCCCCG CAGGGGAAAT CGGCCTGCCC CTACGGAAAT
 CCCGTTTCTT TATACACCCG GTCCTGGCTG GGCGGTGTCT TCCCCGTGGA AGAGAGGGTC
 CGGGAGGTCC GTGGGGCGGA ACAGTCCGAG GGCTTCGGGA GTCAGCCCGG GTGGATTTGT
 TTCGTGGCTC TCGTTGCTGG CTGGGACGGC CGTGTGCCCG TGTTGTTCCG GAGATCGAGG
 CCAACGGATG CCGTACTCTG TCCTCGCCGG GTGCTCAGTG AGGACCCACA GCTGGGCAGG
 GACCCTGGGA GGCCCCTGAG CAAGACTTGG AGGGACGCCC TTGTGCCCCC TGAGCACGTG
 GGGAAGGCGC TGTCCTGGGC CCTGCACCGC TCTGTGTGTT

GeneView

GeneView via analysis of contig annotation: C20orf149 chromosome 20 open reading frame 149

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_011333->NM_024299

function

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


reference	NT_011333->NM_024299->NP_077275	887945	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs310622 maps exactly once on NCBI human chromosome 20

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
20	NW_927339.1	32334781	58831672	minus	G	alt_assembly_1	Celera	Celera	view	400
20	NW_001838671.1	902172	58881518	minus	G	alt_assembly_8	HuRef	HuRef	view	400
20	NT_011333.5	887945	61621759	minus	G	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011333 AL353658

dbSNP Blast Analysis
GenBank HTGS Finished:
AL121829.30

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

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .