Reference SNP(refSNP) Cluster Report: rs2235933

Reference SNP(refSNP) Cluster Report: rs2235933

refSNP ID: rs2235933
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:	Not available
Clinical Association:	unknown

HGVS Names
NM_002403.2:c.519G>A
NM_017459.1:c.519G>A
NP_002394.1:p.A173A
NP_059453.1:p.A173A
NT_004610.18:g.125789C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss52074056 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2235933 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
ss3190168	YUSUKE\|IMS-JST016079	fwd/T	A/G	ggccagcagcggcctgtgccaatccgtggc	gcctcctgtgccaggagctgtgggagctgc	08/07/01	10/10/03	98	Genomic	unknown
ss6802308	WI_SSAHASNP\|NT_030584.7_33964	rev/B	C/T	gcagctcccacagctcctggcacaggaggc	gccacggattggcacaggccgctgctggcc	02/12/03	10/10/03	111	Genomic	unknown
ss13032241	SC_SNP\|NT_030584.9_125790	rev/B	C/T	gcagctcccacagctcctggcacaggaggc	gccacggattggcacaggccgctgctggcc	10/22/03	10/31/03	119	Genomic	unknown
ss52074056	SI_EXO\|NT_004610.17_125790	rev/B	C/T	gcagctcccacagctcctggcacaggaggc	gccacggattggcacaggccgctgctggcc	03/29/06	03/29/06	127	Genomic	unknown
ss84252351	HGSV\|Cor18555_SNV_20070510.chr1_17046754	rev/B	C/T	gcagctcccacagctcctggcacaggaggc	gccacggattggcacaggccgctgctggcc	11/27/07	12/06/07	130	Genomic	unknown
ss87260114	BCMHGSC_JDW\|JWB-0017097	rev/B	C/T	gcagctcccacagctcctggcacaggaggc	gccacggattggcacaggccgctgctggcc	02/26/08	02/26/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGTCCCCGCA GCCTCCGCCG TGTGTACGTC ATTAACAAGG AGATCTGTGT TCGTACAGTG
 TGTGCCCATG AGGAGCTCCT CCGAGGTAGG AAGGCCACCT CCCCAAGACC TCCCCTGTCC
 CCACACCCGC ATCATTATCT GGCCACCTAG CCACCCACCT GATGTTTATT CAACACATAT
 TATCCACCAG GCCCACTTCC AGGACACCCT GAGCTCCCCT CCTTGCTACT TTTCATCCTC
 AAAACACTCC CATCACCAGA GTTGGGGGAG GGGCAGCGGT TCCCATCACC CAGCTCCACC
 CTGACCCTGC CTCCTTCCTG CCCCCAATAG CTGACCTCTG TCGGGACAAG TTCTCCAAAT
 GTGGCGTGAT GGCCAGCAGC GGCCTGTGCC AATCCGTGGC
 R
 GCCTCCTGTG CCAGGAGCTG TGGGAGCTGC TAGGGTGGTG CTGGCATCCT GAGTCCTGGC
 CCTCCTGGGA TCTGGGGCCC TCGGGCCCTG CCTGACCTGG TGCTTTTTTC CCCATCCCCA
 TGTTCCTTTT ATTCTGTAAA AAGTTAGTGG ACTGCAGCCC TGGGGGTTGC AGGCTGCGGT
 GCCTCAGGCC CCTCCTTCAG CCTGTGGCCA CCTCTGGGGC ACAATGGGGG CTCCCCACTG
 CCCAGTCTGC CCCTCGGGTT GGGGGAGTAT CCCAGGCCTC TCTGTGGGAC CTGGGCCCCT
 GACGGGCCTT CTCAGCCCGT TTTGAGGACA GACAGTCCCC CGAGGTAGGC TACATCCCCC
 CACCCCAGCT GGTCTGCTTG GATTTCCTAC AGCCCCCGTG

GeneView

GeneView via analysis of contig annotation: MFAP2 microfibrillar-associated protein 2

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_004610->NM_002403

function

reference

NT_004610->NM_017459

function

HuRef

NW_001838572->NM_002403

function

HuRef

NW_001838572->NM_017459

function

Celera

NW_927841->NM_002403

function

Celera

NW_927841->NM_017459

function

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


reference	NT_004610->NM_002403->NP_002394	125790	reverse	618	synonymous	A	Ala [A]	3	173
					contig reference	G	Ala [A]	3	173

reference	NT_004610->NM_017459->NP_059453	125790	reverse	633	synonymous	A	Ala [A]	3	173
					contig reference	G	Ala [A]	3	173

HuRef	NW_001838572->NM_002403->NP_002394	102907	reverse	618	synonymous	A	Ala [A]	3	173
					contig reference	G	Ala [A]	3	173

HuRef	NW_001838572->NM_017459->NP_059453	102907	reverse	633	synonymous	A	Ala [A]	3	173
					contig reference	G	Ala [A]	3	173

Celera	NW_927841->NM_002403->NP_002394	100229	reverse	618	synonymous	A	Ala [A]	3	173
					contig reference	G	Ala [A]	3	173

Celera	NW_927841->NM_017459->NP_059453	100229	reverse	633	synonymous	A	Ala [A]	3	173
					contig reference	G	Ala [A]	3	173

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2235933 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838572.1	102907	15545530	minus	C	alt_assembly_8	HuRef	HuRef	view	400
1	NW_927841.1	100229	15623786	minus	C	alt_assembly_1	Celera	Celera	view	400
1	NT_004610.18	125790	17174035	minus	C	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_030584

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:
NM_002403.2 NM_017459.1	AL049569.13	AL928903.3 BX284623.2

UniGene Cluster ID
389137

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	G
ss3190168	JBIC-allele		1500	AF		0.553	0.447

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.494+/-0.053	0	0	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .