Reference SNP(refSNP) Cluster Report: rs35941954

Reference SNP(refSNP) Cluster Report: rs35941954

refSNP ID: rs35941954
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:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_015577.1:c.134G>A
NP_056392.1:p.S45N
NT_006576.15:g.34730426G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48411719 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs35941954 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
ss48411719	APPLERA_GI\|hCV25748818		fwd/T	A/G	tggcctcactgctcggcaagaagggggcca	tgccaccaaacacgacagtgagggcaagac	09/28/05	11/03/06	126	Genomic			unknown
ss68932052	PERLEGEN\|PGP17791247		fwd/T	A/G	tggcctcactgctcggcaagaagggggcca	tgccaccaaacacgacagtgagggcaagac	01/30/07	03/31/08	127	Genomic			unknown

Fasta sequence (Legend)

 CACTATTTAT GTTTTCTTTT GGGAAAGCGG CCTTCTTGGG TGTCTCCATG GTGAAGGGGA
 AGGTATTTTA AAACACACTC ATTCGGGAGC AGGCTTTAAT TTGAGTGACA GGAGGGTGGG
 GGCTGCGAGG ACTGCAGCCC TGCTGGTCAG TGCGGCTGTG GCCAGTGTTG TTCATGACCT
 CTGTTTCTTC TCTTTCTCTA CAGACCAATG AGTGGAACAA GAATGATGAC CGGCTACTGC
 AGGCCGTGGA GAATGGAGAT GCGGAGAAGG TGGCCTCACT GCTCGGCAAG AAGGGGGCCA
 R
 TGCCACCAAA CACGACAGTG AGGGCAAGAC CGCGTAAGCT GAAACACTGG TTTGCAGATA
 TGCTGGTTCT GGGTTTTTGG GGTGTTCTCT GGAATCCTTA GTATCCATAG GGGAATTTCA
 CACGTGCTCC CTCTCCACTC CCATGTTGAA ATATGTAAGA AGATATTTTA ATCTAGTGCC
 TTTCTCTCCA AATTCCAAGT CACATATGGA GCTCTACCTT GAATGGGTAT ACATGTTCCC
 AAGTATAAGC AAAGGTTTTA CCTCCTAAGA TTGCAACCAA TTGTAGATGA GACATGAATT

GeneView

GeneView via analysis of contig annotation: RAI14 retinoic acid induced 14

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_015577

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_015577->NP_056392	34730427	forward	245	missense	A	Asn [N]	2	45
					contig reference	G	Ser [S]	2	45

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs35941954 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	349982	34639468	plus	G	alt_assembly_1	Celera	Celera	view	300
5	NW_001838932.2	951114	34706176	minus	C	alt_assembly_8	HuRef	HuRef	view	300
5	NT_006576.15	34730427	34793427	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000005.8

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_015577.1

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss48411719	AGI_ASP population	multiple	78	IG	0.077	0.923	1.000	0.038	0.962

ss68932052	HapMap-CEU	European	120	GF		1.000			1.000

	HapMap-HCB	Asian	90	GF		1.000			1.000

	HapMap-JPT	Asian	90	GF		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.050	0.950		0.025	0.975

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.024+/-0.106	309	249	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 .