Reference SNP(refSNP) Cluster Report: rs1371828

Reference SNP(refSNP) Cluster Report: rs1371828

refSNP ID: rs1371828
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	88/129
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_001083962.1:c.369+17598G>A
NM_003199.2:c.369+17598G>A
NT_025028.13:g.843951C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2158848 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1371828 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
ss2158848	TSC-CSHL\|TSC0524092		fwd/B	C/T	ttgtccagccctgctcaagttctcagggcc	tagaggctcccagtttcaaggcaatcaggc	10/19/00	10/10/03	88	Genomic			95 %

Fasta sequence (Legend)

 CAGGGATTAG AGTCCTTCAT CTTTTGCGAG TCAATGAAAG AATTCACAGC AAAGTTCTGC
 TCCAAGGCTT GTCCAGCCCT GCTCAAGTTC TCAGGGCC
 Y
 TAGAGGCTCC CAGTTTCAAG GCAATCAGGC CATCGCTACT GGGTGCCAAA GCTGCAGAAT
 GTCCACACGG CCACTGCCAT CAGCTCATTC CTGGAAGACA AAGCTGCCTT TCTTCAAGGG
 AAATGTAAGG AGCCATTCAA TCTCAATCTG CATTCATGAC CAACAAGCTG GAGTAGTGCC
 AGAACAGAGC CTGAGACTGG CCACCAACTC TCCAACATCA ACACCTACAC CACATTAGTC
 AAACCAGTAC AGCAGGCCCT ACTCCCAGCG CCTCCCAGGT ACCTCCAGAA GCATGCTGGG
 TCCCCACCCA GGGAGTCCCC ACGGCTCCGC TGAATGAC

GeneView

GeneView via analysis of contig annotation: TCF4 transcription factor 4

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_025028->NM_001083962

function

reference

NT_025028->NM_003199

function

HuRef

NW_001838469->NM_001083962

function

HuRef

NW_001838469->NM_003199

function

Celera

NW_927106->NM_001083962

function

Celera

NW_927106->NM_003199

function

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


reference	NT_025028->NM_001083962->NP_001077431	843951	reverse	intron

reference	NT_025028->NM_003199->NP_003190	843951	reverse	intron

HuRef	NW_001838469->NM_001083962->NP_001077431	846525	reverse	intron

HuRef	NW_001838469->NM_003199->NP_003190	846525	reverse	intron

Celera	NW_927106->NM_001083962->NP_001077431	8364005	reverse	intron

Celera	NW_927106->NM_003199->NP_003190	8364005	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1371828 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_001838469.1	846525	49763176	plus	C	alt_assembly_8	HuRef	HuRef	view	98
18	NW_927106.1	8364005	49770422	plus	C	alt_assembly_1	Celera	Celera	view	98
18	NT_025028.13	843951	51204085	plus	C	ref_assembly	reference	reference	view	98

NCBI Resource Links

Submitter-Referenced

dbSNP Blast Analysis
GenBank HTGS Finished:
AC013587.10 NC_000018.8

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	HWP	C
ss2158848	HapMap-CEU	European	118	IG	1.000		1.000

	HapMap-HCB	Asian	90	IG	1.000		1.000

	HapMap-JPT	Asian	90	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	120	IG	1.000		1.000

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