Reference SNP(refSNP) Cluster Report: rs12898678

Reference SNP(refSNP) Cluster Report: rs12898678

refSNP ID: rs12898678
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	121/129
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_003257.3:c.5152+853G>A
NM_175610.2:c.4912+853G>A
NT_010194.16:g.786130C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss21230688 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12898678 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
ss21230688	SSAHASNP\|WGSA-200403-chr15.chr15.NT_010194.16_786130	fwd/B	C/T	gaggcaggagaatcgcttgaagctgggagg	gaaggttgcagtgagctgagatcgtgccac	03/19/04	03/19/04	121	Genomic	unknown
ss40621962	ABI\|hCV1703605	fwd/B	C/T	gaggcaggagaatcgcttgaagctgggagg	gaaggttgcagtgagctgagatcgtgccac	07/17/05	07/17/05	126	Genomic	unknown
ss70453685	EGP_SNPS\|TJP1-120430	rev/T	A/G	gtggcacgatctcagctcactgcaaccttc	cctcccagcttcaagcgattctcctgcctc	04/18/07	03/31/08	127	Genomic	unknown

Fasta sequence (Legend)

 AAGTCACTCA AGGAAGTGAG AAATGTGAAA ATGCAGTGGA AGCTTTGAAA TTATCTCAGG
 AGAAAAAGTC ATTTACAAAT AGTGTATAAA AGAAGTAATT TAGAGTATTA CACTGAAAAA
 CCATGGCCAA GTATGATCAC AACGGAAGAT CTTGTTAAGT TTCTCTGGTA TACATACGTT
 GTAGATTAAG AAATTAAACA ggccaggcac ggtggctcac acctgtaatc ccagcactct
 gggaggccga ggcgggtgga tcactttaag tcaggagttc gaaccagcct ggccaacatg
 gtgaaacccc gtctctacta aaagtacaaa aattagccag gcatggtggt gggcacctgt
 aatcgaggct gaggcaggag aatcgcttga agctgggagg
 Y
 gaaggttgca gtgagctgag atcgtgccac cgcattccag cctgggcgac agagcgagac
 tccacctcaa aaaaccaaat caaaacaaac aaacaaaaaa TAAATTAAAC AATAGTAACC
 AAAAATAGAA ATAGTTATAT AAAGGAACAA AGTCATTTTA ATAAGGTAAA AATGCCTATT
 TGTGCAGGAC AATATCTCCC ACTGCATCCT GAAAAATTTG ACAGAATAAA TCATTTTTCT
 GAACACCAAG AAATAGTCAA TATTTGGCCA TATTATCAAA AAAAAAtttt tttgagacgg
 tctcgctctg ttgcccaggc tggagtgcag tggcacgatc ttggctcact gcaatctccg
 cctccctggc tcaagcaatt ctcctgcctc agcctcccga gtagctggga ttacaggtgt
 gtgccaccac gcctggctaa tttttgtatt tttagtagag atggggtttc accatgttgg
 tcaggctggt cttgaactcc

GeneView

GeneView via analysis of contig annotation: TJP1 tight junction protein 1 (zona occludens 1)

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_010194->NM_003257

function

reference

NT_010194->NM_175610

function

HuRef

NW_001838199->NM_003257

function

HuRef

NW_001838199->NM_175610

function

Celera

NW_925796->NM_003257

function

Celera

NW_925796->NM_175610

function

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


reference	NT_010194->NM_003257->NP_003248	786130	reverse	intron

reference	NT_010194->NM_175610->NP_783297	786130	reverse	intron

HuRef	NW_001838199->NM_003257->NP_003248	795631	reverse	intron

HuRef	NW_001838199->NM_175610->NP_783297	795631	reverse	intron

Celera	NW_925796->NM_003257->NP_003248	859445	reverse	intron

Celera	NW_925796->NM_175610->NP_783297	859445	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12898678 maps exactly once on NCBI human chromosome 15

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
15	NW_925796.1	859445	7636911	plus	C	alt_assembly_1	Celera	Celera	view	400
15	NW_001838199.1	795631	7660906	plus	C	alt_assembly_8	HuRef	HuRef	view	400
15	NT_010194.16	786130	27782865	plus	C	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010194

dbSNP Blast Analysis
GenBank HTGS Finished:
AC021360.15 AC022613.13 NC_000015.8

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss70453685	EGP_YORUB-PANEL	Sub-Saharan African	24	AF	1.000			1.000

	EGP_HISP-PANEL	Hispanic	44	AF	1.000			1.000

	EGP_CEPH-PANEL	European	44	AF	0.909	0.091		0.955	0.045

	EGP_AD-PANEL	African American	30	AF	1.000			1.000

	EGP_ASIAN-PANEL	Asian	44	AF	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.021+/-0.101	95	95	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .