Reference SNP(refSNP) Cluster Report: rs35317722

Reference SNP(refSNP) Cluster Report: rs35317722

refSNP ID: rs35317722
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	126/129
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
NM_005823.4:c.1462A>G
NM_013404.3:c.1486A>G
NP_005814.2:p.N488D
NP_037536.2:p.N496D
NT_037887.4:g.756973A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48420305 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs35317722 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss48420305	APPLERA_GI\|hCV25996091		fwd/B	C/T	actggatcttcacgaagtattcggacccgt	catgttctggaaagcaaggcgggccttggg	09/28/05	11/30/05	126	Genomic			unknown

Fasta sequence (Legend)

 TTCCTTAGGG ATTCCAGGGC CTGGGTTTGC CTAGCCGCCT GACCCCCAGG CGTGGGAGAC
 CCTGGAGGTG GCTGGCGCCC CGAGCTGGGG TCAGAACCCA CAGCCCCTAA GGCCATACAC
 ACCCCGGGGG GCAGAGGGCG GGTGACCACC CAGTTACCCT GGCAGCAGAC GGCCCGGCGA
 GGCAAAGGCC TGGCACCCCC GAGTGGAGTC TGTGCTTCCC CCGTTGTGTT GCCCACCCTG
 GCCAGGGACT CCCTGGCTCA CCCAGGAAGG ACTGGATCTT CACGAAGTAT TCGGACCCGT
 Y
 CATGTTCTGG AAAGCAAGGC GGGCCTTGGG ATAGAGGACG TCCAGCTGCC TTGGGTCACA
 CGTGTCCAGG TCCTGGGGCC TGACCGCCCT GGGGACACGG TGGGTGGACA GTGAGCGCCA
 GCACACGGAC CCACCTTGCC GGGCAGAGTT CTGGGGACTC ACCAGATGCT GCTGGGGGGC
 ACGGAGCTCA GCTCCTCGGG GCTGAGGGAG CACAGGTACC CAGGGTAGAA GGCGGTCAGG
 GTGTCTAGGG TGTCTTTGTC TAGCTGGCCC CTTCCCTTCA CAAAGCGGTC GATCAGGGTG

GeneView

GeneView via analysis of contig annotation: MSLN mesothelin

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_037887->NM_005823

function

reference

NT_037887->NM_013404

function

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


reference	NT_037887->NM_005823->NP_005814	756974	forward	1513	missense	G	Asp [D]	1	488
					contig reference	A	Asn [N]	1	488

reference	NT_037887->NM_013404->NP_037536	756974	forward	1537	missense	G	Asp [D]	1	496
					contig reference	A	Asn [N]	1	496

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs35317722 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_001838339.2	1884818	739199	plus	T	alt_assembly_8	HuRef	HuRef	view	300
16	NT_037887.4	756974	756974	minus	A	ref_assembly	reference	reference	view	300
16	NW_926018.1	732498	1016848	minus	A	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_005823.4 NM_013404.3	AL031258.12

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/T	T/T	HWP	C	T
ss48420305	AGI_ASP population	multiple	74	IG	0.027	0.973	1.000	0.014	0.986

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.027+/-0.112	38	38	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 .