Reference SNP(refSNP) Cluster Report: rs16991389

Reference SNP(refSNP) Cluster Report: rs16991389

refSNP ID: rs16991389
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	123/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001003828.1:c.212-33357C>A
NM_013327.3:c.113-33357C>A
NT_011521.4:g.560051C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss80015448 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16991389 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
ss23597953	PERLEGEN\|afd0138521	fwd/T	A/C	ttagggtgagttatacctgatgggacttaa	tgggtaaatgtcatctagtaacccaactac	08/10/04	09/13/04	123	Genomic	unknown
ss66133585	AFFY\|SNP_A-2081134	fwd/T	A/C	acctgatgggacttaa	tgggtaaatgtcatct	10/27/06	03/31/08	127	Genomic	unknown
ss76142845	AFFY\|AFFY_6_1M_SNP_A-2081134	fwd/T	A/C	acctgatgggacttaa	tgggtaaatgtcatct	08/28/07	08/30/07	129	Genomic	unknown
ss80015448	HGSV\|Cor18507_SNV_20070510.chr22_42781352	fwd/T	A/C	ttagggtgagttatacctgatgggacttaa	tgggtaaatgtcatctagtaacccaactac	11/23/07	11/24/07	130	Genomic	unknown

Fasta sequence (Legend)

 CCAAGATCTG AGGCAAGGGA ATCGTTTTCA ATAGGAAACT TTTAAATGTT TGAGCAGCAG
 AAAGGGAGAT TGAGCCAGAA GAACTTGCTG GTGGAAAGAT GGTGGAAGCT GGGAGCTTTG
 AGGTTCTAAA AATCCTGGTG TGTCAGGTCA GGTAGTGGGG CAACCGGAGC TTAGGGTGAG
 TTATACCTGA TGGGACTTAA
 M
 TGGGTAAATG TCATCTAGTA ACCCAACTAC ATTCGGCATT AATATCTGGA CAAAAGGTGG
 AATACACCCG GGTTCTTTGG GCACAGGCGA AGGAGAGGTC TCATAGTTTG ATGTTGCTCA
 AGAAGGGAAA ACAAGCAGGA TGGGAAGAGG TCTAATCAGC CGGCTGGAGT GGGGTGCTGG
 GTTTAGTTCA TTCCTTCTTA

GeneView

GeneView via analysis of contig annotation: PARVB parvin, beta

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_011521->NM_001003828

function

reference

NT_011521->NM_013327

function

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


reference	NT_011521->NM_001003828->NP_001003828	560051	forward	intron

reference	NT_011521->NM_013327->NP_037459	560051	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs16991389 maps exactly once on NCBI human chromosome 22

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
22	NW_001838749.1	569477	27410286	plus	C	alt_assembly_8	HuRef	HuRef	view	100
22	NW_927650.1	1547654	28368021	plus	C	alt_assembly_1	Celera	Celera	view	100
22	NT_011521.4	560051	42787784	plus	C	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000022.5

dbSNP Blast Analysis
GenBank HTGS Finished:
Z82178.2

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/C	C/C	HWP	A	C
ss23597953	AFD_EUR_PANEL	European	48	IG	0.042	0.958	1.000	0.021	0.979

	AFD_AFR_PANEL	African American	46	IG	0.217	0.783	0.584	0.109	0.891

	AFD_CHN_PANEL	Asian	48	IG		1.000			1.000

	HapMap-CEU	European	120	IG	0.017	0.983	1.000	0.008	0.992

	HapMap-HCB	Asian	88	IG		1.000			1.000

	HapMap-JPT	Asian	90	IG		1.000			1.000

	HapMap-YRI	Sub-Saharan African	118	IG	0.288	0.712	0.200	0.144	0.856

ss66133585	HapMap-CEU	European	118	GF	0.017	0.983		0.008	0.992

	HapMap-HCB	Asian	90	GF		1.000			1.000

	HapMap-JPT	Asian	90	GF		1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.300	0.700		0.150	0.850

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.084+/-0.187	332	260	269	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .