Reference SNP(refSNP) Cluster Report: rs3810484

Reference SNP(refSNP) Cluster Report: rs3810484

refSNP ID: rs3810484
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
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_001037335.2:c.6072T>C
NM_033405.3:c.4365T>C
NP_001032412.2:p.P2024P
NP_208384.3:p.P1455P
NT_011333.5:g.930732A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss69380672 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3810484 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
ss4996890	YUSUKE\|IMS-JST170267	fwd/T	A/G	attcaggccagggccgaggctgctgggccc	gggcgtgggctggccgtgggagccggcagc	08/12/02	10/10/03	107	Genomic	unknown
ss8311157	SC_SNP\|NT_011333.5_930733	fwd/T	A/G	attcaggccagggccgaggctgctgggccc	gggcgtgggctggccgtgggagccggcagc	04/17/03	11/18/03	114	Genomic	unknown
ss17702703	CSHL-HAPMAP\|CSHL-HuCC-200402.chr20.NT_011333.5_930733	fwd/T	A/G	attcaggccagggccgaggctgctgggccc	gggcgtgggctggccgtgggagccggcagc	02/19/04	03/04/04	120	Genomic	unknown
ss48421437	APPLERA_GI\|hCV25941721	rev/B	C/T	gctgccggctcccacggccagcccacgccc	gggcccagcagcctcggccctggcctgaat	09/28/05	11/03/06	126	Genomic	unknown
ss69380672	SI_EXO\|NT_011333.5_930733	fwd/T	A/G	attcaggccagggccgaggctgctgggccc	gggcgtgggctggccgtgggagccggcagc	04/12/07	04/12/07	127	Genomic	unknown
ss78659023	HGSV\|Cor12878_SNV_20070510.chr20_61664547	fwd/T	A/G	attcaggccagggccgaggctgctgggccc	gggcgtgggctggccgtgggagccggcagc	10/17/07	10/20/07	129	Genomic	unknown
ss85801272	HGSV\|Cor19129_SNV_20070510.chr20_61664547	fwd/T	A/G	attcaggccagggccgaggctgctgggccc	gggcgtgggctggccgtgggagccggcagc	12/06/07	12/10/07	130	Genomic	unknown

Fasta sequence (Legend)

 TCCTCTAGTC CACGCACGGC TTCCTCCTTG CGGCTGGGGG TGAAGGCAGA CACTGGAAAA
 CCAACAGGAC TCCCAGGAAA GGGGCTGCTG CCCCACGAGC TCCCCCCTCC TGCAAGTGAG
 GGGCCCGGGG CGGTCCCCCA GCCCAGCCTC TGCTGGTGGA AGCCACTCAC AGATCAGGAA
 GCTGCTTGGG CAGCAGCTCA ACGGTGAACA GGGTGCCCGG CCTCAGCACC TCTTCCGGAA
 CCTTCTCCAT GCCCATGTGG TGGACGAAGA GGTGCACCCG TCTGGGAGCC TCCTGCCGGT
 CTGCCCGGCG CTCCTGGTCC CAGTCCTGCG TCTGCCCGTG GGCCACCCAG GTATACGTGC
 CGGGGTCAAC ATTCAGGCCA GGGCCGAGGC TGCTGGGCCC
 R
 GGGCGTGGGC TGGCCGTGGG AGCCGGCAGC CCCTCGAGCC GGATGCAGAG GTAGCAGCAG
 CTGAAGTTGA TGTCGGCACA GTTCTCCTCG AGGAAGGCGG CCTCCAGGCG GAAGGCGCCC
 TGCAGCTGCC CCTGCGGCGT CCGTGACGCC TCCCAGGAGA CACTCAGGTG CTGAAGTGTG
 ACGGAGTCAT TCTCGGCAAC CGCGCCGGTG GCCGACTCCA GGGCGCAGAA TGGTTCCCAC
 ACGCAGGCGT ACTCATCCAC GTCGCGGTAC CGGTCCCTCG GGGCCCGGTA CACACGGCCT
 GAGAAGCAGT CTCCGGGCCG CTCCACGTGC TCCAGGCAGA GGCTGAAGCC CGGTGCCACC
 GTCCAGAGCT GAGGGCTCGG TACCAGGAAG CCGTGCTGCA

GeneView

GeneView via analysis of contig annotation: PRIC285 peroxisomal proliferator-activated receptor A interacting complex 285

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_001037335

function

reference

NT_011333->NM_033405

function

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


reference	NT_011333->NM_001037335->NP_001032412	930733	reverse	6964	synonymous	C	Pro [P]	3	2024
					contig reference	T	Pro [P]	3	2024

reference	NT_011333->NM_033405->NP_208384	930733	reverse	4469	synonymous	C	Pro [P]	3	1455
					contig reference	T	Pro [P]	3	1455

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3810484 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	32377572	58874463	plus	A	alt_assembly_1	Celera	Celera	view	400
20	NW_001838671.1	944993	58924339	plus	A	alt_assembly_8	HuRef	HuRef	view	400
20	NT_011333.5	930733	61664547	plus	A	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011333.5

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:
NM_001037335.2 NM_033405.3	AL121829.30

UniGene Cluster ID
517180

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss48421437	AGI_ASP population	multiple	42	IG	0.429	0.238	0.333	0.020	0.548	0.452

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.495+/-0.047	35	35	0	0

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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .