Reference SNP(refSNP) Cluster Report: rs16902944

Reference SNP(refSNP) Cluster Report: rs16902944

refSNP ID: rs16902944
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:	C/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_145000.2:c.91+376C>G
NT_006576.15:g.36273809G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss85257779 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs16902944 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
ss23415578	PERLEGEN\|afd3106928	fwd/T	C/G	acaaacttaggcttaaacaaagtgaaaaaa	tgtcccaccagtggtactatggtagagaaa	08/10/04	09/13/04	123	Genomic	unknown
ss66116422	AFFY\|SNP_A-2026493	fwd/T	C/G	aaacaaagtgaaaaaa	tgtcccaccagtggta	10/27/06	03/31/08	127	Genomic	unknown
ss76103616	AFFY\|AFFY_6_1M_SNP_A-2026493	fwd/	C/G	aaacaaagtgaaaaaa	tgtcccaccagtggta	08/28/07	08/30/07	129	Genomic	unknown
ss85257779	HGSV\|Cor18517_SNV_20070510.chr5_36336809	fwd/	C/G	acaaacttaggcttaaacaaagtgaaaaaa	tgtcccaccagtggtactatggtagagaaa	12/06/07	12/08/07	130	Genomic	unknown

Fasta sequence (Legend)

 AAAGACTGAT GGTGAAAATG GCTGGGAGGT AGATAGTTTA GTTTGAATGA GTGCCCAGCA
 AGTGAAATGT GACACTTTTC CCTGACTGTC TCCAGATGTC CCTGGACCAT AAAAAGGAAA
 GAGTCAAGAA TATATTTATT TTTCCCACAA TGAATGAGCC AGAGATCCAG ACAAACTTAG
 GCTTAAACAA AGTGAAAAAA
 S
 TGTCCCACCA GTGGTACTAT GGTAGAGAAA GCTCCAGGCT AACTTAAAGC TACTCTCAGC
 TGAAATCCCC CTTGTAGCTG ACTCAGCCTT GCTCAGATGG GTGTTTTGAA TTAGACAAAA
 TCTAGCATAC TCTAAAAAAC ACAGTGGCTA GAAGTTTAAG CATGTAAGTT TCAGAATGAC
 AGCTCCAAGG AATATGCATT

GeneView

GeneView via analysis of contig annotation: RANBP3L RAN binding protein 3-like

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_006576->NM_145000

function

HuRef

NW_001838933->NM_145000

function

Celera

NW_922596->NM_145000

function

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


reference	NT_006576->NM_145000->NP_659437	36273809	reverse	intron

HuRef	NW_001838933->NM_145000->NP_659437	595303	reverse	intron

Celera	NW_922596->NM_145000->NP_659437	1897237	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs16902944 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_922596.1	1897237	36186723	plus	G	alt_assembly_1	Celera	Celera	view	100
5	NW_001838933.1	595303	36252692	plus	G	alt_assembly_8	HuRef	HuRef	view	100
5	NT_006576.15	36273809	36336809	plus	G	ref_assembly	reference	reference	view	100

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000005.5

dbSNP Blast Analysis
GenBank HTGS Finished:
AC026439.4 AC114277.2 NC_000005.8

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss23415578	AFD_EUR_PANEL	European	48	IG			1.000			1.000

	AFD_AFR_PANEL	African American	46	IG	0.087	0.435	0.478	1.000	0.304	0.696

	AFD_CHN_PANEL	Asian	48	IG			1.000			1.000

	HapMap-CEU	European	114	IG			1.000			1.000

	HapMap-HCB	Asian	88	IG			1.000			1.000

	HapMap-JPT	Asian	80	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	118	IG	0.153	0.492	0.356	0.527	0.398	0.602

ss66116422	HapMap-CEU	European	118	GF			1.000			1.000

	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	0.033	0.417	0.550		0.242	0.758

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss23415578	307	6	35	255
ss66116422	244	2	28	214

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs16902944	332	6	38	265

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5134	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19127	YOR077.02	r23_ch5_YRI_affymetrix:genechip500k	2851204
5134	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19127	YOR077.02	chr5-HapMap-YRI
5135	ss23415578	C/C	CSHL-HAPMAP	HapMap-YRI	NA19128	YOR077.03	r23_ch5_YRI_affymetrix:genechip500k	2851204
5135	ss66116422	C/G	CSHL-HAPMAP	HapMap-YRI	NA19128	YOR077.03	chr5-HapMap-YRI
5136	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19132	YOR101.01	r23_ch5_YRI_affymetrix:genechip500k	2851204
5136	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19132	YOR101.01	chr5-HapMap-YRI
5137	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	r23_ch5_YRI_affymetrix:genechip500k	2851204
5137	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	chr5-HapMap-YRI
5139	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r23_ch5_YRI_affymetrix:genechip500k	2851204
5139	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	chr5-HapMap-YRI
5140	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19099	YOR105.02	r23_ch5_YRI_affymetrix:genechip500k	2851204
5140	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19099	YOR105.02	chr5-HapMap-YRI
5141	ss23415578	C/C	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	r23_ch5_YRI_affymetrix:genechip500k	2851204
5141	ss66116422	C/G	CSHL-HAPMAP	HapMap-YRI	NA19098	YOR105.03	chr5-HapMap-YRI
5143	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19193	YOR112.02	r23_ch5_YRI_affymetrix:genechip500k	2851204
5143	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19193	YOR112.02	chr5-HapMap-YRI
5238	ss23415578	C/C	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	r23_ch5_YRI_affymetrix:genechip500k	2851204
5238	ss66116422	C/G	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	chr5-HapMap-YRI
5241	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	r23_ch5_YRI_affymetrix:genechip500k	2851204
5241	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	chr5-HapMap-YRI
5245	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA18858	YOR012.02	r23_ch5_YRI_affymetrix:genechip500k	2851204
5245	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA18858	YOR012.02	chr5-HapMap-YRI
5246	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA18859	YOR012.03	r23_ch5_YRI_affymetrix:genechip500k	2851204
5246	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA18859	YOR012.03	chr5-HapMap-YRI
5250	ss23415578	C/C	CSHL-HAPMAP	HapMap-YRI	NA18521	YOR016.01	r23_ch5_YRI_affymetrix:genechip500k	2851204
5250	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA18521	YOR016.01	chr5-HapMap-YRI
5252	ss23415578	C/C	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	r23_ch5_YRI_affymetrix:genechip500k	2851204
5252	ss66116422	C/G	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	chr5-HapMap-YRI
5255	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA18871	YOR017.03	r23_ch5_YRI_affymetrix:genechip500k	2851204
5255	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA18871	YOR017.03	chr5-HapMap-YRI
5259	ss23415578	C/C	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	r23_ch5_YRI_affymetrix:genechip500k	2851204
5259	ss66116422	C/G	CSHL-HAPMAP	HapMap-YRI	NA18857	YOR023.01	chr5-HapMap-YRI
5260	ss23415578	C/C	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	r23_ch5_YRI_affymetrix:genechip500k	2851204
5260	ss66116422	C/G	CSHL-HAPMAP	HapMap-YRI	NA18855	YOR023.02	chr5-HapMap-YRI
5269	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19093	YOR040.02	r23_ch5_YRI_affymetrix:genechip500k	2851204
5269	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19093	YOR040.02	chr5-HapMap-YRI
5275	ss23415578	C/C	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	r23_ch5_YRI_affymetrix:genechip500k	2851204
5275	ss66116422	C/G	CSHL-HAPMAP	HapMap-YRI	NA19137	YOR043.02	chr5-HapMap-YRI
5276	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	r23_ch5_YRI_affymetrix:genechip500k	2851204
5276	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	chr5-HapMap-YRI
5285	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	r23_ch5_YRI_affymetrix:genechip500k	2851204
5285	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19203	YOR048.03	chr5-HapMap-YRI
5292	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19161	YOR056.01	r23_ch5_YRI_affymetrix:genechip500k	2851204
5292	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19161	YOR056.01	chr5-HapMap-YRI
5297	ss23415578	C/C	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	r23_ch5_YRI_affymetrix:genechip500k	2851204
5297	ss66116422	C/G	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	chr5-HapMap-YRI
5300	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19119	YOR060.03	r23_ch5_YRI_affymetrix:genechip500k	2851204
5300	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19119	YOR060.03	chr5-HapMap-YRI
5302	ss23415578	C/G	CSHL-HAPMAP	HapMap-YRI	NA19140	YOR071.02	r23_ch5_YRI_affymetrix:genechip500k	2851204
5302	ss66116422	G/G	CSHL-HAPMAP	HapMap-YRI	NA19140	YOR071.02	chr5-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	269

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 .