Reference SNP(refSNP) Cluster Report: rs4646400

Reference SNP(refSNP) Cluster Report: rs4646400

refSNP ID: rs4646400
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	111/129
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_007169.2:c.94-149G>A
NM_148172.1:c.205-149G>A
NM_148173.1:c.94-149G>A
NT_010718.15:g.17023207C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss12404541 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4646400 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
ss6311486	RIKENSNPRC\|ssj0003688		fwd/T	A/G	ttgctctagggcagataatgtgcagctggg	tgcatgtggttgttgctcccgtgtaattct	01/15/03	10/10/03	111	Genomic			unknown
ss12404541	WI_SSAHASNP\|chr17.NT_010718.13_16264995		rev/B	C/T	agaattacacgggagcaacaaccacatgca	cccagctgcacattatctgccctagagcaa	07/04/03	10/25/06	116	Genomic			unknown

Fasta sequence (Legend)

 AGGGCCTGAG GTCAGACCCC ATGTGTCTCC CCAGGGACAG ATCTTCTCCA CCAGACGTCT
 CTTTCTGCCT CTTGGTGGGT TCATGGCTGT GTCTGGTTGA AGAGTTGTTT CCAGAAGGAC
 CTTGTTGTCC GTCCAGATGA ACTGAGCAAG TGTGAAAATC CCTGTGGAAC TTGCTCTAGG
 GCAGATAATG TGCAGCTGGG
 R
 TGCATGTGGT TGTTGCTCCC GTGTAATTCT TCTTCTTTGG AAATGGGGGC TTTGGAGCCT
 GGGAAGCAGA GAGAGGCATG TGCTCCCCAC CCCCACCCTG GAGTCTCCCC AGGAAATATC
 TCGTTCTTGT TCTCTGCTCA CGGTTTAGGT TGCACGATGG GAACACAAGA CCCGCAAGCT
 GAGCAGGGCC TTCGGATCCC

GeneView

GeneView via analysis of contig annotation: PEMT phosphatidylethanolamine N-methyltransferase

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_010718->NM_007169

function

reference

NT_010718->NM_148172

function

reference

NT_010718->NM_148173

function

HuRef

NW_001838410->NM_007169

function

HuRef

NW_001838410->NM_148172

function

HuRef

NW_001838410->NM_148173

function

Celera

NW_926628->NM_007169

function

Celera

NW_926628->NM_148172

function

Celera

NW_926628->NM_148173

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_010718->NM_007169->NP_009100	17023207	reverse	intron

reference	NT_010718->NM_148172->NP_680477	17023207	reverse	intron

reference	NT_010718->NM_148173->NP_680478	17023207	reverse	intron

HuRef	NW_001838410->NM_007169->NP_009100	909511	forward	intron

HuRef	NW_001838410->NM_148172->NP_680477	909511	forward	intron

HuRef	NW_001838410->NM_148173->NP_680478	909511	forward	intron

Celera	NW_926628->NM_007169->NP_009100	670490	reverse	intron

Celera	NW_926628->NM_148172->NP_680477	670490	reverse	intron

Celera	NW_926628->NM_148173->NP_680478	670490	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs4646400 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838410.2	909511	17178720	plus	G	alt_assembly_8	HuRef	HuRef	view	200
17	NT_010718.15	17023207	17366583	minus	C	ref_assembly	reference	reference	view	200
17	NW_926628.1	670490	18365280	minus	C	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010718

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC020558.4 NC_000017.9	AC090608.8

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss12404541	HapMap-CEU	European	116	IG		0.069	0.931	1.000	0.034	0.966

	HapMap-HCB	Asian	88	IG	0.045	0.273	0.682	0.584	0.182	0.818

	HapMap-JPT	Asian	86	IG	0.023	0.163	0.814	0.403	0.105	0.895

	HapMap-YRI	Sub-Saharan African	106	IG	0.019	0.340	0.642	0.439	0.189	0.811

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.217+/-0.248	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 .