Reference SNP(refSNP) Cluster Report: rs17880808

Reference SNP(refSNP) Cluster Report: rs17880808

refSNP ID: rs17880808
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	124/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	A
Clinical Association:	unknown

HGVS Names
NM_003150.3:c.372+108A>G
NM_139276.2:c.372+108A>G
NM_213662.1:c.372+108A>G
NT_010755.15:g.4221765T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss69380276 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs17880808 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
ss28526937	PGA-UW-FHCRC\|STAT3-045048		fwd/T	A/G	agatctactaaaaaagaaggaaaagaaatt	aatagatcaataatcataaaaatacattga	11/05/04	11/05/04	124	Genomic			unknown
ss69380276	SI_EXO\|NT_010755.15_4221765		rev/B	C/T	tcaatgtatttttatgattattgatctatt	aatttcttttccttcttttttagtagatct	04/12/07	04/12/07	127	Genomic			unknown

Fasta sequence (Legend)

 TACAGAAATA GTAACGACCT CCCCTTCGCC CCCCGCCGAC AGAGAGCCTT CACCCAGGCT
 CTGAAGCCTT TGTTCCGTTG TTTCCTAGAA TAAATGCTTT CCTTGATGAA TACATTAGTT
 TTAAGGTGCC ACAGTTCAGT CCACATCTCC ATGGTCTGCT GCTGATTTTT ATTCTCTTTC
 TCTCCTACTT ATAGAGCAGG TATCTTGAGA AGCCAATGGA GATTGCCCGG ATTGTGGCCC
 GGTGCCTGTG GGAAGAATCA CGCCTTCTAC AGACTGCAGC CACTGCGGCC CAGGTGAGAC
 CTGAGACAAA ACAAATCCCT GGTCTGGGAG GAATGGAAAA TCAAACAACT TTATAATGAG
 ATAAATTATT AGATCTACTA AAAAAGAAGG AAAAGAAATT
 R
 AATAGATCAA TAATCATAAA AATACATTGA AAAACTCTAA AAAAAAAGAA AGTTCCACCC
 CCCAAAATAC ATTGAAAAAC TCTAAAAAAA AGAAAGTTCC ACCAAAAGAA TCCAACAGAC
 CCAATGGTTT AAAAGTTTTG TTTTGTTCTG ACAAATTTTC TTTGTTTTTC TTTTTTTTTT
 TTTCTGAGAC AGAGTTTTGC TCTTGTTACC CAGGCTAGAG TGCAATGGCG CGATCTTGGC
 TCACTGCAAC CTCCACCTCC AGGGTTCAAG TGATTCTCCT GCCTCAGCCT CAAGAGTAGC
 TGGGATTATA GGCGTGTGCC ACCACACCCA GCTAATTTTG TATTTTTAGT AGAGACGGGG
 TTTCTTCATG TTGGTCAGGC TGGTCTCGAA CTCCTGACCT

GeneView

GeneView via analysis of contig annotation: STAT3 signal transducer and activator of transcription 3 (acute-phase response factor)

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_010755->NM_003150

function

reference

NT_010755->NM_139276

function

reference

NT_010755->NM_213662

function

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


reference	NT_010755->NM_003150->NP_003141	4221765	reverse	intron

reference	NT_010755->NM_139276->NP_644805	4221765	reverse	intron

reference	NT_010755->NM_213662->NP_998827	4221765	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs17880808 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_001838436.2	901785	36261940	plus	A	alt_assembly_8	HuRef	HuRef	view	400
17	NW_926828.1	4022984	37151793	minus	T	alt_assembly_1	Celera	Celera	view	400
17	NT_010755.15	4221765	37750995	minus	T	ref_assembly	reference	reference	view	400

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010755.15

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss28526937	PGA-AFRICAN-PANEL	African American	48	IG	1.000			1.000

	PGA-EUROPEAN-PANEL	European	46	IG	0.957	0.043	1.000	0.978	0.022

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.021+/-0.100	47	26	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 .