Reference SNP(refSNP) Cluster Report: rs478919

Reference SNP(refSNP) Cluster Report: rs478919

refSNP ID: rs478919
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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_000926.3:c.1789+405G>A
NT_033899.7:g.4558749C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss16343376 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs478919 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
ss648436	SC_JCM\|AP001316.2_73395	rev/T	A/G	agaaaaatggtagttgacacatatgtacat	tatgcgtatacatatttgtacatacacgaa	07/27/00	10/10/03	83	Genomic	unknown
ss1776825	KWOK\|OVLP-000925-308054	fwd/B	C/T	ttcgtgtatgtacaaatatgtatacgcata	atgtacatatgtgtcaactaccatttttct	10/05/00	10/10/03	87	Genomic	99 %
ss1777932	KWOK\|OVLP-000925-319696	fwd/B	C/T	ttcgtgtatgtacaaatatgtatacgcata	atgtacatatgtgtcaactaccatttttct	10/05/00	10/10/03	87	Genomic	99 %
ss1778800	KWOK\|OVLP-000925-332801	fwd/B	C/T	ttcgtgtatgtacaaatatgtatacgcata	atgtacatatgtgtcaactaccatttttct	10/05/00	10/10/03	87	Genomic	99 %
ss1779565	KWOK\|OVLP-000925-342527	fwd/B	C/T	ttcgtgtatgtacaaatatgtatacgcata	atgtacatatgtgtcaactaccatttttct	10/05/00	10/10/03	87	Genomic	99 %
ss16343376	EGP_SNPS\|PGR-006926	rev/T	A/G	agaaaaatggtagttgacacatatgtacat	tatgcgtatacatatttgtacatacacgaa	01/16/04	04/07/04	120	Genomic	unknown

Fasta sequence (Legend)

 TTAAAGCAAA ATACTTCTTT AGAAATTATG TTACTGTGAT GTCCAGGTTT TTTATTTTAA
 ACTGTTTAAT CCTGTCCTCT TATACACTTA CAAAAATATA CTGAACAAAA AGAGAATTCA
 AAAATTTGTT TAGAATTACT TCTTTGTAAA TATTACATAA ATATTCATGT AGTCAAAAGA
 CAGTATCATG TAGAAAACTG CATCATATAC ATGTTGTGAT ATATGTTCGT GTATGTACAA
 ATATGTATAC GCATA
 Y
 ATGTACATAT GTGTCAACTA CCATTTTTCT TTTAATCAAA ATTTTAAAGT ACTGCATACA
 CATATACCTA CATAATAGAT ATATAAAAGT ACTATTAGAA CAAAGCTGTT TCCTCAAAGC
 TAAGCAGTTA AGGAACAATA GTAGCACTGT CCTCAAGATT TTTATGACTT ATGTCTAATA
 CTGAAAGTGT TAGTCAAAGA GTATGCAATT ATAGTACCCA ACCACATTCC ATTTTGAGTA
 TCATAAATAA AAACA

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

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


reference	NT_033899->NM_000926->NP_000917	4558749	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs478919 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	19753593	96933416	minus	G	alt_assembly_8	HuRef	HuRef	view	255
11	NW_925173.1	11034582	98165682	plus	C	alt_assembly_1	Celera	Celera	view	255
11	NT_033899.7	4558749	100501543	plus	C	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
AY525610 AC020735 AP000625 AP000625.2 AP000638 AP000638.2 AP001316.2 AP001533 AP001533.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AP001533.4	AP000625.2 AP000638.2 AP001316.2

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss16343376	PDR90	Global	172	IG	0.942	0.058	1.000	0.971	0.029

ss648436	SC_12_A	Asian	22	IG	1.000			1.000

	SC_12_AA	African American	24	IG	0.917	0.083	1.000	0.958	0.042

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.054+/-0.155	114	114	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 .