Reference SNP(refSNP) Cluster Report: rs519792

Reference SNP(refSNP) Cluster Report: rs519792

refSNP ID: rs519792
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
Map to Genome Build:	36.3

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

HGVS Names
NM_000926.3:c.2213-5212A>T
NT_033899.7:g.4489927T>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2955286 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs519792 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
ss690102	SC_JCM\|AP001919.2_165001	fwd/T	A/T	catgtaattgaaacagataatctacaacaa	ggcagagcattaaatatctcagcaccttct	07/27/00	10/10/03	83	Genomic	unknown
ss1776799	KWOK\|OVLP-000925-308011	fwd/T	A/T	catgtaattgaaacagataatctacaacaa	ggcagagcattaaatatctcagcaccttct	10/05/00	10/10/03	92	Genomic	99 %
ss1777898	KWOK\|OVLP-000925-319647	fwd/T	A/T	catgtaattgaaacagataatctacaacaa	ggcagagcattaaatatctcagcaccttct	10/05/00	10/10/03	87	Genomic	99 %
ss2955286	TSC-CSHL\|TSC1063827	fwd/T	A/T	catgtaattgaaacagataatctacaacaa	ggcagagcattaaatatctcagcaccttct	01/29/01	10/25/06	94	Genomic	unknown
ss10674016	BCM_SSAHASNP\|chr11.NT_033899.5_4471355	fwd/T	A/T	catgtaattgaaacagataatctacaacaa	ggcagagcattaaatatctcagcaccttct	06/29/03	10/10/03	116	Genomic	unknown
ss16144350	SC_SNP\|NT_033899.6_4471363	fwd/T	A/T	catgtaattgaaacagataatctacaacaa	ggcagagcattaaatatctcagcaccttct	11/18/03	11/22/03	120	Genomic	unknown
ss23628922	PERLEGEN\|afd1740114	fwd/T	A/T	catgtaattgaaacagataatctacaacaa	ggcagagcattaaatatctcagcaccttct	08/10/04	09/13/04	123	Genomic	unknown
ss38676888	ABI\|hCV539508	fwd/	A/T	catgtaattgaaacagataatctacaacaa	ggcagagcattaaatatctcagcaccttct	07/16/05	07/16/05	126	Genomic	unknown
ss88742610	BCMHGSC_JDW\|JWB-0469803	fwd/	A/T	catgtaattgaaacagataatctacaacaa	ggcagagcattaaatatctcagcaccttct	02/26/08	02/27/08	129	Genomic	unknown

Fasta sequence (Legend)

 TGACAGAATG GAATAGAACT CAGAAAATAA CCTTTATTTA CTCCACCTTT TACAGTGCTT
 ATCTGTGATA AATGTACAAT GTTAAATTGA CTTGAACATG CCTAGTATAG AAATGCTATT
 TTTTTCCTTA TTAACTGTAA TATCATTCAT TACTTTATGC TGAAACAAAG ATGGGAACAC
 AGAGATTAAA TTCCCAGTGA TGATAATGAT CAGGTAAACT TAGTACATTT GAGATGACCA
 AAATGAAAAA CCTTCACATG GAGAAGTGAT GGATTATCAC TAATTGTGTT TAACAAATGT
 TAAAAAAAAA AACACTTTTC CTTTTAAGTG ACTTGACCTG ATAATTTCTG ACAAAAGCCC
 TGTTACAGCT GTCCAAATTT AGCTTAAAGA ATTAACAGAA AGTATATAGT GAAGAGATGG
 CCTGGggctg ggtgtggtgg ctcatgcccg tagtcccagt gctttgggag gcgaggcagg
 agagtcactt gaggccagga atttgagacc agccaagacc cagtctctac aaaccaattt
 aaaaagcttg tccaggtgtg gtggtgcaca cctgtagtgc tggggaggct gaagttactg
 gggaggctga agcaggacga tggcttgagc ccaggagttc taagctgccg tgagctacaa
 tcatgccact gcactccagc ctgggtgaca gagtgagagc ctatctcaag aaaaaaaaaa
 aaaaaaaaGA TGGCCTGTAT GACAGTACTA CTAAGTTCCC CAATCTTACT CCCAGAGTTT
 TGATAAAATA TGTAGGTTTT GGTTCTGTAA AAAATGTCAT GTAATTGAAA CAGATAATCT
 ACAACAA
 W
 GGCAGAGCAT TAAATATCTC AGCACCTTCT GACACAAAGC AACAACTTTC ATACACAAGT
 ATCAATGTTG AGAAGCACAA AGAAGCTTCA ATATGATTAA GTATAATCAC CAACGTATGT
 TTGATGATTT ATGCTGAATA AGAAGTTAAT GTCTAATAAT CTAAGGTAGT ACAGTTCTTT
 GCAAATCAAT TCTGTAATTT AAA

GeneView

GeneView via analysis of contig annotation: PGR progesterone receptor

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_033899->NM_000926

function

HuRef

NW_001838042->NM_000926

function

Celera

NW_925173->NM_000926

function

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


reference	NT_033899->NM_000926->NP_000917	4489927	reverse	intron

HuRef	NW_001838042->NM_000926->NP_000917	19822416	forward	intron

Celera	NW_925173->NM_000926->NP_000917	10965761	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs519792 maps exactly once on NCBI human chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NW_001838042.2	19822416	96864593	minus	A	alt_assembly_8	HuRef	HuRef	view	847
11	NW_925173.1	10965761	98096861	plus	T	alt_assembly_1	Celera	Celera	view	847
11	NT_033899.7	4489927	100432721	plus	T	ref_assembly	reference	reference	view	847

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033899 AC020735 AP000625 AP000625.2 AP001316 AP001316.2 AP001533

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AP001533.4 NC_000011.8	AC020735.5 AP001316.2 AP001919.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/T	T/T	HWP	A	T
ss23628922	AFD_EUR_PANEL	European	48	IG	0.625	0.333	0.042	1.000	0.792	0.208

	AFD_AFR_PANEL	African American	46	IG	0.348	0.391	0.261	0.317	0.543	0.457

	AFD_CHN_PANEL	Asian	48	IG	1.000				1.000

ss2955286	HapMap-CEU	European	114	IG	0.474	0.509	0.018	0.050	0.728	0.272

	HapMap-HCB	Asian	88	IG	1.000				1.000

	HapMap-JPT	Asian	86	IG	1.000				1.000

	HapMap-YRI	Sub-Saharan African	114	IG	0.140	0.596	0.263	0.150	0.439	0.561

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.356+/-0.226	332	260	9	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .