Reference SNP(refSNP) Cluster Report: rs2561818

Reference SNP(refSNP) Cluster Report: rs2561818

refSNP ID: rs2561818
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
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_152403.2:c.2233G>A
NM_182798.1:c.1531G>A
NM_182799.1:c.331G>A
NP_689616.2:p.V745M
NP_877950.1:p.V511M
NP_877951.1:p.V111M
NT_006576.15:g.38408061G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3596023 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2561818 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
ss3596023	SC_JCM\|AC010457.6_4907	fwd/T	A/G	ttcattggcggagtccccaattatgatgat	tgaagaagaactcgggtgtcctgaagcctt	09/24/01	10/10/03	100	Genomic	unknown
ss74819197	AFFY\|SNP_M-319582	fwd/T	A/G	ttcattggcggagtccccaattatgatgat	tgaagaagaactcgggtgtcctgaagcctt	08/09/07	08/09/07	128	Genomic	unknown
ss74894757	ILLUMINA\|ILMN_Human_1M_rs2561818	fwd/T	A/G	ttcattggcggagtccccaattatgatgat	tgaagaagaactcgggtgtcctgaagcctt	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 TAGACAGATT GTCATGATGG GTCTCGAGGC TCTGTCTACC ATTTTGTTCC CCAACAGGGA
 ACTGAAGACA CATTTGATCA TTTTGAACAT CTGTTTTAAA GTCATACAAT GCTTTGTTTT
 TAATCTTTTG GCAGGGAGGC TTCACACAGA TTAAGTGCAA CACAGACATT TTCATTGGCG
 GAGTCCCCAA TTATGATGAT
 R
 TGAAGAAGAA CTCGGGTGTC CTGAAGCCTT TCAGCGGGAG CATCCAGAAG GTACAGGCAT
 CTCTTCCTCA TGTTTACTGG GCCACCCAGA CTGTAGACAA AGAAAGTGAG GATTATGATC
 AGTGTCATCT GCTGCACCCA AGAAAGACAC TTTGAGAAAG TTTTAACATT TTTAAAAATT
 TCTATTTTAA TGCCCACAGC

GeneView

GeneView via analysis of contig annotation: EGFLAM EGF-like, fibronectin type III and laminin G domains

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_006576->NM_152403

function

reference

NT_006576->NM_182798

function

reference

NT_006576->NM_182799

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_006576->NM_152403->NP_689616	38408062	forward	2557	missense	A	Met [M]	1	745
					contig reference	G	Val [V]	1	745

reference	NT_006576->NM_182798->NP_877950	38408062	forward	1872	missense	A	Met [M]	1	511
					contig reference	G	Val [V]	1	511

reference	NT_006576->NM_182799->NP_877951	38408062	forward	1038	missense	A	Met [M]	1	111
					contig reference	G	Val [V]	1	111

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2561818 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_922596.1	4032399	38321885	plus	G	alt_assembly_1	Celera	Celera	view	200
5	NW_001838933.1	2730401	38387790	plus	G	alt_assembly_8	HuRef	HuRef	view	200
5	NT_006576.15	38408062	38471062	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AC010457 AC090076

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_152403.2 NM_182798.1 NM_182799.1

UniGene Cluster ID
20103

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss3596023	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	0.017	0.983	1.000	0.008	0.992

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.005+/-0.049	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 .