Reference SNP(refSNP) Cluster Report: rs10828395

Reference SNP(refSNP) Cluster Report: rs10828395

refSNP ID: rs10828395
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NM_173081.2:c.1877G>A
NP_775104.1:p.R626Q
NT_008705.15:g.5272576G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss86055129 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10828395 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
ss15777171	SC_SNP\|NT_008705.15_5272577	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	11/17/03	11/22/03	120	Genomic	unknown
ss17385388	CSHL-HAPMAP\|CSHL-HuCC-200402.chr10.NT_008705.15_5272577	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	02/19/04	10/26/06	120	Genomic	unknown
ss18870119	SC_SNP\|SC-CHR9-12_NA07340-200402.chr10.NT_008705.15_5272577	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	02/20/04	03/04/04	120	Genomic	unknown
ss24456071	PERLEGEN\|afd2222275	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	08/10/04	09/13/04	123	Genomic	unknown
ss28508220	MGC_GENOME_DIFF\|BC039312x37551352-G5272577A	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	08/25/04	08/25/04	126	cDNA	unknown
ss38580819	ABI\|hCV1885773	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	07/15/05	11/02/06	126	Genomic	unknown
ss66539967	ILLUMINA\|HumanHap300v1.1_rs10828395	fwd/B	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	11/09/06	11/09/06	127	Genomic	unknown
ss66903272	ILLUMINA\|HumanHap550v1.1_rs10828395	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	11/14/06	11/14/06	127	Genomic	unknown
ss67025016	ILLUMINA\|HumanHap650Yv1.0_rs10828395	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	11/14/06	11/14/06	127	Genomic	unknown
ss69073998	PERLEGEN\|PGP02222275	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	01/30/07	03/31/08	127	Genomic	unknown
ss70381223	ILLUMINA\|HumanHap300v2.0_rs10828395	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	04/18/07	11/18/07	127	Genomic	unknown
ss70500743	ILLUMINA\|HumanHap550v3.0__rs10828395	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	04/20/07	03/30/08	130	Genomic	unknown
ss71026629	ILLUMINA\|HumanHap650Yv3.0_rs10828395	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	04/23/07	04/23/07	127	Genomic	unknown
ss74811530	AFFY\|SNP_M-185580	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	08/09/07	08/09/07	128	Genomic	unknown
ss75680817	ILLUMINA\|ILMN_Human_1M_rs10828395	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	08/28/07	08/29/07	129	Genomic	unknown
ss76894213	SI_EXO\|NT_008705.15_5272577	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	09/20/07	09/20/07	129	Genomic	unknown
ss85009191	KRIBB_YJKIM\|KHS873304	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	12/04/07	12/08/07	130	Genomic	unknown
ss86055129	HGSV\|Cor18517_SNV_20070510.chr10_23337258	fwd/T	A/G	tggaagataaatcagatgttggttatggac	aagtatttcttcttcatcttccttaagaag	12/06/07	12/11/07	130	Genomic	unknown

Fasta sequence (Legend)

 TCTTCTTGCA GTGGCTCATG CCTATAATCC CAACCCTTTG TGAGGTTGAT GCAGGAGGAT
 CCTTTGAGCT CAGGAGTTTG AGAGCAGCTT GGGCAACACG GTGAAACCCC ATCTATACAA
 AAAATACAAA AATTAGCTGG GTATGGTAGC ACATGCCTGT AGTCCCAGCT ACTTGGGGGA
 CTGAGGTGGG AGGATCGCTT GAGCCCCGGA GGTCAAGGCT GCAGTGAGCC ATCATCGCAC
 CACTGCACTC CAGCCTGGGC GATAGAGTGA GATCCTGTCT CAAAAAACAA ACAAAGAAAA
 AATGACTTCT CCTTTATACT TTAAAAACAG TATGTCACTG TTAAAAGTCA GCTTCAGTTA
 TGACTTTCAG AAAAAAATCT GTTTCGTGGA ATAAAACCAT CTGTTGACAA ATAATTTTAA
 TCTATATATA ATTTTAAATG TGTAAAATTT TAGTTCTCCA CCTTCATCTA TGGAAGATAA
 ATCAGATGTT GGTTATGGAC
 R
 AAGTATTTCT TCTTCATCTT CCTTAAGAAG ATCAAGTAAA GAAAAGAACA AGTAAGAAAA
 TGATGTTTTA TCTGTATGCA AACAGCTTCC CCTTTAATTT GAGTGTGAAA AAATGTTTTA
 GATTTTAGAT TGGGGCAACT TGATTTTTAT TCTTCTTATG GTAATACAAT TGCATAATTG
 CCTTTTACAT TGCTATGGGA AAGATCTCTG GAATAGGAGC CAGGAAATCT GGTTTCACCT
 TCTATTTCGC CCTGTGGACC TGCAGTGATT TGGGCCACAT GACTTAGTGT CTGTGTGGGT
 TTCGTTTCCT TAGCTGTGGA CGAAATAACA CCGGGTCCCT GGCTTCATCA TGGGGAAAGG
 AATCAAGTTA TATAATGAAG TAAAAAT

GeneView

GeneView via analysis of contig annotation: ARMC3 armadillo repeat containing 3

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_008705->NM_173081

function

HuRef

NW_001837931->NM_173081

function

Celera

NW_924584->NM_173081

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_008705->NM_173081->NP_775104	5272577	forward	1954	missense	A	Gln [Q]	2	626
					contig reference	G	Arg [R]	2	626

HuRef	NW_001837931->NM_173081->NP_775104	7823854	reverse	1954	missense	A	Gln [Q]	2	626
					contig reference	G	Arg [R]	2	626

Celera	NW_924584->NM_173081->NP_775104	22984897	forward	1954	missense	A	Gln [Q]	2	626
					contig reference	G	Arg [R]	2	626

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs10828395 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_001837931.2	7823854	22958123	minus	C	alt_assembly_8	HuRef	HuRef	view	500
10	NW_924584.1	22984897	22984897	plus	G	alt_assembly_1	Celera	Celera	view	500
10	NT_008705.15	5272577	23337258	plus	G	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008705.15 BC039312

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL139815.12 NC_000010.9	AC022247.2

UniGene Cluster ID
137270

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G	N
ss17385388	HapMap-CEU	European	120	IG	0.050	0.267	0.683	0.403	0.183	0.817

	HapMap-HCB	Asian	90	IG		0.111	0.889	0.752	0.056	0.944

	HapMap-JPT	Asian	88	IG		0.182	0.818	0.527	0.091	0.909

	HapMap-YRI	Sub-Saharan African	120	IG	0.100	0.433	0.467	1.000	0.317	0.683

	CHMJ	Asian	74	IG					0.068	0.905	0.027

ss24456071	AFD_EUR_PANEL	European	48	IG	0.083	0.417	0.500	1.000	0.292	0.708

	AFD_AFR_PANEL	African American	46	IG	0.130	0.304	0.565	0.251	0.283	0.717

	AFD_CHN_PANEL	Asian	46	IG		0.304	0.696	0.403	0.152	0.848

ss38580819	AoD_African_American		90	AF					0.320	0.680

	AoD_Caucasian		92	AF					0.240	0.760

	AoD_Chinese		90	AF					0.130	0.870

	AoD_Japanese		90	AF					0.130	0.870

ss69073998	HapMap-CEU	European	120	GF	0.050	0.267	0.683		0.183	0.817

	HapMap-HCB	Asian	90	GF		0.111	0.889		0.056	0.944

	HapMap-JPT	Asian	90	GF		0.178	0.822		0.089	0.911

	HapMap-YRI	Sub-Saharan African	120	GF	0.133	0.383	0.483		0.325	0.675

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss17385388	262	13	70	178
ss24456071	71	5	24	41
ss69073998	262	13	70	179

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs10828395	332	17	90	216

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
151	ss17385388	A/G	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	r23_ch10_CEU_bcm:genotype_0002
151	ss69073998	G/G	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	chr10-HapMap-CEU
5139	ss17385388	A/G	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r23_ch10_YRI_bcm:genotype_0002
5139	ss69073998	A/A	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	chr10-HapMap-YRI
5140	ss17385388	G/G	CSHL-HAPMAP	HapMap-YRI	NA19099	YOR105.02	r23_ch10_YRI_bcm:genotype_0002
5140	ss69073998	A/G	CSHL-HAPMAP	HapMap-YRI	NA19099	YOR105.02	chr10-HapMap-YRI
5243	ss17385388	A/G	CSHL-HAPMAP	HapMap-YRI	NA18507	YOR009.03	r23_ch10_YRI_bcm:genotype_0002
5243	ss69073998	A/A	CSHL-HAPMAP	HapMap-YRI	NA18507	YOR009.03	chr10-HapMap-YRI
5287	ss17385388	A/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	r23_ch10_YRI_bcm:genotype_0002
5287	ss69073998	G/G	CSHL-HAPMAP	HapMap-YRI	NA19209	YOR050.02	chr10-HapMap-YRI
5289	ss17385388	A/G	CSHL-HAPMAP	HapMap-YRI	NA19208	YOR051.01	r23_ch10_YRI_bcm:genotype_0002
5289	ss69073998	A/A	CSHL-HAPMAP	HapMap-YRI	NA19208	YOR051.01	chr10-HapMap-YRI
5291	ss17385388	A/G	CSHL-HAPMAP	HapMap-YRI	NA19207	YOR051.03	r23_ch10_YRI_bcm:genotype_0002
5291	ss69073998	A/A	CSHL-HAPMAP	HapMap-YRI	NA19207	YOR051.03	chr10-HapMap-YRI
5293	ss17385388	A/G	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	r23_ch10_YRI_bcm:genotype_0002
5293	ss69073998	G/G	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	chr10-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

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 .