Reference SNP(refSNP) Cluster Report: rs2138018

Reference SNP(refSNP) Cluster Report: rs2138018

refSNP ID: rs2138018
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	96/129
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_000547.3:c.820-682A>G
NM_175719.1:c.820-682A>G
NM_175721.1:c.820-682A>G
NM_175722.1:c.820-8192A>G
NT_022221.12:g.204112A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss3064149 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2138018 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
ss3064149	TSC-CSHL\|TSC1153174	fwd/T	A/G	tcccaggaaacctgtaaatctggaaaaaat	ttttagatctccatgttacagatgagaaga	06/07/01	10/10/03	96	Genomic	unknown
ss11516267	WI_SSAHASNP\|chr2.NT_033000.5_185692	fwd/T	A/G	tcccaggaaacctgtaaatctggaaaaaat	ttttagatctccatgttacagatgagaaga	07/03/03	10/10/03	116	Genomic	unknown
ss14484670	WUGSC_SSAHASNP\|chr2.NT_033000.6_204112	fwd/T	A/G	tcccaggaaacctgtaaatctggaaaaaat	ttttagatctccatgttacagatgagaaga	11/05/03	11/22/03	119	Genomic	unknown
ss37043874	EGP_SNPS\|TPO-064920	fwd/T	A/G	tcccaggaaacctgtaaatctggaaaaaat	ttttagatctccatgttacagatgagaaga	04/20/05	11/02/06	125	Genomic	unknown
ss44184998	ABI\|hCV16133860	fwd/T	A/G	tcccaggaaacctgtaaatctggaaaaaat	ttttagatctccatgttacagatgagaaga	07/18/05	07/18/05	126	Genomic	unknown

Fasta sequence (Legend)

 CTATTACGAG AAGACCGTGA TCTTCAGGAA GAGTCTCTTT CGGAATCTGT CCAACCCCGG
 TGATCTTGTG ATTCTGGATG AGCGATTTAA CCTCCTAAAT CTGATAACGC CCAGGGTAGG
 CCCTGACCCC GTGACACCTC ACCAGGGAGG AAGAGCTGAC AGGGAAAGGG CACATGCTCT
 CTGCAGCCCA CAGAGCTCGA CTCTTCCCAG GAAACCTGTA AATCTGGAAA AAAT
 R
 TTTTAGATCT CCATGTTACA GATGAGAAGA TGGAAGCTGG CCACAGCCAG AGTTGGAATC
 CCACCCAAGG TCTCCTCACT CCCCTCAAGC TGCCTTTACA CTAAACAGTG ATGCCCACAA
 AACTCGGAGA CTGTTTACTC ATTGTGCTCC TAAACCAAGT CCATGGCACT GGAAAGGAAG
 AAGTCAGCTC TTCCGAAAGT CAGAAAATAA ACCAGACCGG GGATTCCATG AGCAGCTAGA
 GCAGGTCTGA GCAGGAGCGA GACTGGCTCA GGCCAAGAGC GTCTGAGCTT TGGGGAGATG
 TGGACTCCTA GGATGTGGGG TCCATCCTCT GGGTTCAACC TCTTCCAGGC AAGAGACCAC
 CAGTGAGCAG G

GeneView

GeneView via analysis of contig annotation: TPO thyroid peroxidase

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_022221->NM_000547

function

reference

NT_022221->NM_175719

function

reference

NT_022221->NM_175721

function

reference

NT_022221->NM_175722

function

HuRef

NW_001838759->NM_000547

function

HuRef

NW_001838759->NM_175719

function

HuRef

NW_001838759->NM_175721

function

HuRef

NW_001838759->NM_175722

function

Celera

NW_927719->NM_000547

function

Celera

NW_927719->NM_175719

function

Celera

NW_927719->NM_175721

function

Celera

NW_927719->NM_175722

function

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


reference	NT_022221->NM_000547->NP_000538	204112	forward	intron

reference	NT_022221->NM_175719->NP_783650	204112	forward	intron

reference	NT_022221->NM_175721->NP_783652	204112	forward	intron

reference	NT_022221->NM_175722->NP_783653	204112	forward	intron

HuRef	NW_001838759->NM_000547->NP_000538	192253	forward	intron

HuRef	NW_001838759->NM_175719->NP_783650	192253	forward	intron

HuRef	NW_001838759->NM_175721->NP_783652	192253	forward	intron

HuRef	NW_001838759->NM_175722->NP_783653	192253	forward	intron

Celera	NW_927719->NM_000547->NP_000538	1460303	forward	intron

Celera	NW_927719->NM_175719->NP_783650	1460303	forward	intron

Celera	NW_927719->NM_175721->NP_783652	1460303	forward	intron

Celera	NW_927719->NM_175722->NP_783653	1460303	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2138018 maps exactly once on NCBI human chromosome 2

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
2	NT_022221.12	204112	1459183	plus	A	ref_assembly	reference	reference	view	234
2	NW_001838759.1	192253	1470639	plus	A	alt_assembly_8	HuRef	HuRef	view	234
2	NW_927719.1	1460303	1528368	plus	A	alt_assembly_1	Celera	Celera	view	234

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033000

dbSNP Blast Analysis
GenBank HTGS Finished:
AC105450.1 AC108489.5 NC_000002.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss37043874	EGP_YORUB-PANEL	Sub-Saharan African	24	IG		0.833	0.167	0.020	0.417	0.583

	EGP_HISP-PANEL	Hispanic	44	IG	0.136	0.455	0.409	1.000	0.364	0.636

	EGP_CEPH-PANEL	European	44	IG	0.182	0.273	0.545	0.100	0.318	0.682

	EGP_AD-PANEL	African American	30	IG	0.133	0.067	0.800	0.005	0.167	0.833

	EGP_ASIAN-PANEL	Asian	48	IG	0.208	0.333	0.458	0.200	0.375	0.625

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.443+/-0.159	95	95	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: BCM_SSAHASNP, NCBI

UNKNOWN

YES

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Revised: May 25, 2006 1:38 PM .