Reference SNP(refSNP) Cluster Report: rs1242390

Reference SNP(refSNP) Cluster Report: rs1242390

refSNP ID: rs1242390
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_007169.2:c.355+1229A>G
NM_148172.1:c.466+1229A>G
NM_148173.1:c.355+1229A>G
NT_010718.15:g.17011943T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3305478 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1242390 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
ss1872913	KWOK\|OVLP-000925-114465	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	10/06/00	10/10/03	87	Genomic	99 %
ss2498741	SC_JCM\|AC020558.3_17175	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	11/03/00	04/07/04	92	Genomic	unknown
ss3305478	TSC-CSHL\|TSC1470637	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	09/20/01	10/10/03	100	Genomic	unknown
ss6311500	RIKENSNPRC\|ssj0003702	rev/T	A/G	ctgtagggagtttggtccaggaagggggac	gcagccaggagcgtctggatctgccaggtg	01/15/03	10/10/03	111	Genomic	unknown
ss6809014	WI_SSAHASNP\|NT_030843.4_152940	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	02/12/03	10/10/03	111	Genomic	unknown
ss16752667	CSHL-HAPMAP\|CSHL-HuAA-200402.chr17.NT_010718.14_16255600	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	02/17/04	03/04/04	120	Genomic	unknown
ss17587304	CSHL-HAPMAP\|CSHL-HuCC-200402.chr17.NT_010718.14_16255600	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	02/19/04	03/04/04	120	Genomic	unknown
ss19368939	CSHL-HAPMAP\|CSHL-HuDD-200402.chr17.NT_010718.14_16255600	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	02/20/04	03/04/04	120	Genomic	unknown
ss21427933	SSAHASNP\|WGSA-200403-chr17.chr17.NT_010718.14_16255600	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	03/19/04	03/20/04	121	Genomic	unknown
ss77295021	HGSV\|Cor12156_SNV_20070510.chr17_17355319	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	10/09/07	10/12/07	129	Genomic	unknown
ss78176985	HGSV\|Cor12878_SNV_20070510.chr17_17355319	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	10/17/07	10/18/07	129	Genomic	unknown
ss90550990	BCMHGSC_JDW\|JWB-1007966	fwd/B	C/T	cacctggcagatccagacgctcctggctgc	gtcccccttcctggaccaaactccctacag	02/26/08	02/29/08	129	Genomic	unknown

Fasta sequence (Legend)

 CGGAGTCCCC CTTCCCATGG GGCCCTCACC GCCCTCACAT CCTGGAAGGG CCCCTCCACA
 GCTCCTCCTG AGCCCCACCT CTGATCCTGG CTCCATCGGT CCAACCTCTT CCTTGCTGGG
 ACCCCCCCTA TGGCTCCCAC CTCTCTGGGG ATGGAGCCTC AGCCCCTTGG ATGGCCTTCA
 AGGCCTCGGC TCATCCTCCT GCCCTGTCCC AACCGACAGC ACCTGTGCGG CCAGTCCAGC
 TGCCCCCCAC CTCCAGCTGC CAGCTACTCT GCCCTCAACC TCCCTCTCCT TGCACCAAGG
 CTTTTTTCTC TTTCCTACCT GCCCGCACCT GCCCCCACCT GGCAGATCCA GACGCTCCTG
 GCTGC
 Y
 GTCCCCCTTC CTGGACCAAA CTCCCTACAG CGTCTGCCTG AGCAGGAAGC ACTGAACTGC
 CTGTGGGTGC CCCCCACAGT CCCAGAGAGG CCTGGCCATG GGCGATCCAG AATGCTGCAC
 CCACAGATGC CACTTCCTCC CTCGGGGGGA CCCCTACTGG CAGGCACAAG CTCCTTGAGA
 ACTTGGAGTG CCCTGTGACA GCCCACGGTG CCCTGGGGGC TGGGCC

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

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


reference	NT_010718->NM_007169->NP_009100	17011943	reverse	intron

reference	NT_010718->NM_148172->NP_680477	17011943	reverse	intron

reference	NT_010718->NM_148173->NP_680478	17011943	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1242390 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	920775	17167456	minus	G	alt_assembly_8	HuRef	HuRef	view	365
17	NT_010718.15	17011943	17355319	plus	T	ref_assembly	reference	reference	view	365
17	NW_926628.1	659226	18354016	plus	C	alt_assembly_1	Celera	Celera	view	365

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010718 AC073621 AC073621.3

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss2498741	SC_12_A	Asian	24	IG	0.833	0.167	1.000	0.917	0.083

	SC_12_AA	African American	24	IG	1.000			1.000

	SC_12_C	European	14	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.062+/-0.165	36	25	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: NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .