Reference SNP(refSNP) Cluster Report: rs10193983

Reference SNP(refSNP) Cluster Report: rs10193983

refSNP ID: rs10193983
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
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.95-3534G>A
NM_175719.1:c.95-3534G>A
NM_175721.1:c.95-3534G>A
NM_175722.1:c.95-3534G>A
NT_022221.12:g.147219G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14058280 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10193983 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
ss14058280	WUGSC_SSAHASNP\|chr2.NT_033000.6_147219	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	11/05/03	10/25/06	119	Genomic	unknown
ss20101200	CSHL-HAPMAP\|CSHL-HuFF-200402.chr2.NT_033000.6_147219	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	02/21/04	03/04/04	120	Genomic	unknown
ss21607153	SSAHASNP\|WGSA-200403-chr2.chr2.NT_033000.6_147219	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	03/20/04	03/20/04	121	Genomic	unknown
ss41564393	ABI\|hCV356128	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	07/17/05	07/17/05	126	Genomic	unknown
ss66823867	ILLUMINA\|HumanHap300v1.1_rs10193983	fwd/B	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	11/09/06	11/09/06	127	Genomic	unknown
ss66875296	ILLUMINA\|HumanHap550v1.1_rs10193983	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	11/14/06	11/14/06	127	Genomic	unknown
ss66958063	ILLUMINA\|HumanHap650Yv1.0_rs10193983	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	11/14/06	11/14/06	127	Genomic	unknown
ss68801094	PERLEGEN\|PGP04894838	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	01/30/07	03/31/08	127	Genomic	unknown
ss70361574	ILLUMINA\|HumanHap300v2.0_rs10193983	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	04/18/07	11/17/07	127	Genomic	unknown
ss70470873	ILLUMINA\|HumanHap550v3.0__rs10193983	rev/B	C/T	ttctgttggagagggaaatggtcacttttg	ggatttatgttctacttttaggcaatagag	04/20/07	03/29/08	130	Genomic	unknown
ss70992593	ILLUMINA\|HumanHap650Yv3.0_rs10193983	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	04/23/07	04/23/07	127	Genomic	unknown
ss74845828	AFFY\|SNP_M-604756	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	08/09/07	08/09/07	128	Genomic	unknown
ss75909109	ILLUMINA\|ILMN_Human_1M_rs10193983	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	08/28/07	08/29/07	129	Genomic	unknown
ss84920061	KRIBB_YJKIM\|KHS848543	fwd/T	A/G	ctctattgcctaaaagtagaacataaatcc	caaaagtgaccatttccctctccaacagaa	12/04/07	12/08/07	130	Genomic	unknown

Fasta sequence (Legend)

 AGTCCCGTGA CTCCCTAGAA CTCAGTGTTC AGTTCTGAAA AAAAACTTCG GGTTCAAACT
 CCCTAAGTCT ATGGTCCTTG CATCAGACGC CTCTTCCCTG GGATTGCTGG GAACTGAGGA
 AGGAAGGGCG CTGCAGAGCT AACGATAGCA AGGGGCTCAG AGCTGGCCAC CCCAGCTCCC
 TGGTGGCAGG AGAGCTAATG tgagctgatg gaaactgaga agcagcagat aaaggaaaag
 ccatctgccc tgcctctatt gcctaaaagt agaacataaa tcc
 R
 caaaagtgac catttccctc tccaacagaa aggacagaaa ttcatcacca gggaccccag
 gccctcaaca gcctggaacc agccccagag gcatttgtgt ggcaaacctc tgcagccccg
 gcctcccttc ctgtagttgc cccagagagg cctcctcaaa acgtgtttcc tgggaactca
 aagtcctttg ctttggtctt gcagcttctt ggaaaatgat tgttcttttg ctgaggggct
 gtgcagcaga gttctaacga tccattcgag tttccatctt ggggcgctca gggggctccc
 tcgtggaagc aggagtccag gctaataacc cctgtgagtt ttcctcctgt gactctgcct
 tttgtcagtc taatttcaat gccccagaaa attaatctaa gatgcaggga gagaaaaggt
 ttcttcttcc cctacaGATG GATGTCAGTC ATCTCTATTC AGCCAAGAAG TAGTTAACCT
 AAACAATGAA AACACCACCG

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	147219	forward	intron

reference	NT_022221->NM_175719->NP_783650	147219	forward	intron

reference	NT_022221->NM_175721->NP_783652	147219	forward	intron

reference	NT_022221->NM_175722->NP_783653	147219	forward	intron

HuRef	NW_001838759->NM_000547->NP_000538	136060	forward	intron

HuRef	NW_001838759->NM_175719->NP_783650	136060	forward	intron

HuRef	NW_001838759->NM_175721->NP_783652	136060	forward	intron

HuRef	NW_001838759->NM_175722->NP_783653	136060	forward	intron

Celera	NW_927719->NM_000547->NP_000538	1404674	forward	intron

Celera	NW_927719->NM_175719->NP_783650	1404674	forward	intron

Celera	NW_927719->NM_175721->NP_783652	1404674	forward	intron

Celera	NW_927719->NM_175722->NP_783653	1404674	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10193983 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	147219	1402290	plus	G	ref_assembly	reference	reference	view	283
2	NW_001838759.1	136060	1414446	plus	A	alt_assembly_8	HuRef	HuRef	view	283
2	NW_927719.1	1404674	1472739	plus	G	alt_assembly_1	Celera	Celera	view	283

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033000

dbSNP Blast Analysis
GenBank HTGS Finished:
AC105450.1 AC108462.5 AC108489.5 AC140476.2 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
ss14058280	HapMap-CEU	European	120	IG	0.033	0.200	0.767	0.317	0.133	0.867

	HapMap-HCB	Asian	90	IG		0.178	0.822	0.527	0.089	0.911

	HapMap-JPT	Asian	88	IG	0.023	0.023	0.955	0.001	0.034	0.966

	HapMap-YRI	Sub-Saharan African	118	IG	0.034	0.407	0.559	0.343	0.237	0.763

ss68801094	HapMap-CEU	European	120	GF	0.033	0.200	0.767		0.133	0.867

	HapMap-HCB	Asian	90	GF		0.178	0.822		0.089	0.911

	HapMap-JPT	Asian	90	GF	0.022	0.044	0.933		0.044	0.956

	HapMap-YRI	Sub-Saharan African	120	GF	0.033	0.417	0.550		0.242	0.758

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.232+/-0.249	270	210	270	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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .