Reference SNP(refSNP) Cluster Report: rs319682

Reference SNP(refSNP) Cluster Report: rs319682

refSNP ID: rs319682
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
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_002375.3:c.2323-1528T>C
NM_030884.2:c.1528-1528T>C
NT_022517.17:g.47855122A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44427759 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs319682 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
ss409202	KWOK\|OVLP-000621-267054	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	06/30/00	10/10/03	79	Genomic	99 %
ss904217	KWOK\|OVLP-000804-167238	rev/B	C/T	tttccagcagagctggtagcagaaccactt	ccctgattccagccttagcgttcttcacac	09/01/00	04/07/04	86	Genomic	99 %
ss1590495	KWOK\|OVLP-000925-254443	rev/B	C/T	tttccagcagagctggtagcagaaccactt	ccctgattccagccttagcgttcttcacac	10/04/00	10/25/06	87	Genomic	99 %
ss2514819	SC_JCM\|AC023910.10_122280	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	11/03/00	10/10/03	92	Genomic	unknown
ss3647359	SC_JCM\|AC016928.16_90784	rev/B	C/T	tttccagcagagctggtagcagaaccactt	ccctgattccagccttagcgttcttcacac	09/24/01	10/10/03	100	Genomic	unknown
ss10093007	BCM_SSAHASNP\|chr3.NT_005825.15_5605755	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	06/27/03	10/10/03	116	Genomic	unknown
ss11604242	WI_SSAHASNP\|chr3.NT_005825.15_5605755	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	07/03/03	10/10/03	116	Genomic	unknown
ss14238328	BCM_SSAHASNP\|chr3.NT_022517.16_47840710	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	11/05/03	10/21/04	119	Genomic	unknown
ss20182578	CSHL-HAPMAP\|CSHL-HuFF-200402.chr3.NT_022517.16_47840710	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	02/21/04	03/04/04	120	Genomic	unknown
ss22003725	SSAHASNP\|WGSA-200403-chr3.chr3.NT_022517.16_47840710	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	03/20/04	03/20/04	121	Genomic	unknown
ss24296966	PERLEGEN\|afd2359101	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	08/10/04	09/13/04	123	Genomic	unknown
ss44427759	ABI\|hCV2166522	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	07/18/05	11/03/06	126	Genomic	unknown
ss65718456	ILLUMINA\|Human1-rs319682	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	10/10/06	10/10/06	127	Genomic	unknown
ss68374159	CSHL-HAPMAP\|perlegen:assay:25184.2359101:1	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	01/11/07	01/16/07	127	NA	unknown
ss75018777	ILLUMINA\|ILMN_Human_1M_rs319682	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	08/28/07	08/29/07	129	Genomic	unknown
ss84462480	HGSV\|Cor19129_SNV_20070510.chr3_47890122	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	12/06/07	12/07/07	130	Genomic	unknown
ss92080944	BCMHGSC_JDW\|JWB-1589625	fwd/T	A/G	gtgtgaagaacgctaaggctggaatcaggg	aagtggttctgctaccagctctgctggaaa	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 CTACGGGGAT AGGGGATGAA GACACTATTT TGATAAACAA ATTACCACAT TACAAAAGAG
 AGTATGCCAA ATCACAGACA CAGTGGGCTC AGCTCTCTTC CTCCAAGAGA AGTGGCTATA
 AAGAGGGCAG TATGTAGGTA GCGACAAGCA GGATATCGTT AAATGGAAAA ATCAGCTAAG
 GAGGTACTAG AAATTAAGGG CTGGCATCCA AAGTCTAACT CTGCAAATGT AGGGTAATGA
 CAATTTCCAC AAATAAAGGC CTTAAGTATG GTGTGAAGAA CGCTAAGGCT GGAATCAGGG
 R
 AAGTGGTTCT GCTACCAGCT CTGCTGGAAA CATGTAGGAT TTTGGCCAGA GGATTCCCTT
 TTCTATTGCT CTAAAATTTG AGGACTAAAC CAGATGCTCT CTGGGATGTG CATCAAATTT
 TTAAGACTAT GACTATTATT CAGAATAATC TAGCATAGTC TTATTATTTT GCCATGAGGG
 TAATAATGAT AAAATAAGTT AGAAAAAAGT TATGTGGGAT AGAAATCTCA AAAGGATGTT
 GCATCTTTTA GATGTCAGGC TCTTGGCTTC AAAAACCTGC AGAAGTTAAC TGGAGCTATT

GeneView

GeneView via analysis of contig annotation: MAP4 microtubule-associated protein 4

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_022517->NM_002375

function

reference

NT_022517->NM_030884

function

HuRef

NW_001838877->NM_002375

function

HuRef

NW_001838877->NM_030884

function

Celera

NW_921651->NM_002375

function

Celera

NW_921651->NM_030884

function

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


reference	NT_022517->NM_002375->NP_002366	47855122	reverse	intron

reference	NT_022517->NM_030884->NP_112146	47855122	reverse	intron

HuRef	NW_001838877->NM_002375->NP_002366	18297373	forward	intron

HuRef	NW_001838877->NM_030884->NP_112146	18297373	forward	intron

Celera	NW_921651->NM_002375->NP_002366	47865010	reverse	intron

Celera	NW_921651->NM_030884->NP_112146	47865010	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs319682 maps exactly once on NCBI human chromosome 3

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
3	NW_921651.1	47865010	47865010	plus	G	alt_assembly_1	Celera	Celera	view	300
3	NT_022517.17	47855122	47890122	plus	A	ref_assembly	reference	reference	view	300
3	NW_001838877.2	18297373	47970289	minus	C	alt_assembly_8	HuRef	HuRef	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_022517 AC016928 AC023910 AC023910.10 AC023910.9 AC023911

dbSNP Blast Analysis

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
ss14238328	CHMJ	Asian	74	IG					0.743	0.216	0.041

ss24296966	AFD_EUR_PANEL	European	48	IG	0.375	0.417	0.208	0.527	0.583	0.417

	AFD_AFR_PANEL	African American	46	IG	0.130	0.565	0.304	0.439	0.413	0.587

	AFD_CHN_PANEL	Asian	48	IG	0.667	0.250	0.083	0.251	0.792	0.208

ss44427759	HapMap-CEU	European	120	IG	0.350	0.500	0.150	0.752	0.600	0.400

	HapMap-HCB	Asian	90	IG	0.533	0.356	0.111	0.371	0.711	0.289

	HapMap-JPT	Asian	88	IG	0.545	0.409	0.045	0.584	0.750	0.250

	HapMap-YRI	Sub-Saharan African	120	IG	0.183	0.433	0.383	0.479	0.400	0.600

	AoD_African_American		90	AF					0.380	0.620

	AoD_Caucasian		92	AF					0.740	0.260

ss904217	SC_12_A	Asian	22	IG	0.455	0.364	0.182	0.479	0.636	0.364

	SC_12_AA	African American	24	IG	0.167	0.417	0.417	0.752	0.375	0.625

	SC_12_C	European	12	IG	0.667	0.167	0.167	0.200	0.750	0.250

	SC_95_C	European	76	IG	0.316	0.500	0.184	1.000	0.566	0.434

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss24296966	71	28	29	14
ss44427759	268	94	118	55
ss904217	123

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs319682	401	118	143	68

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
187	ss904217	C/T	TSC-CSHL	SC_95_C	CEPH1341.14		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
187	ss44427759	A/A	CSHL-HAPMAP	HapMap-CEU	NA06985	CEPH1341.14	r23_ch3_CEU_illumina:golden_gate_1.0.0
229	ss904217	C/T	TSC-CSHL	SC_95_C	CEPH1347.02		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
229	ss904217	T/T	TSC-CSHL	SC_12_C	CEPH1347.02		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE
229	ss44427759	A/G	CSHL-HAPMAP	HapMap-CEU	NA10859	CEPH1347.02	r23_ch3_CEU_illumina:golden_gate_1.0.0
230	ss904217	C/T	TSC-CSHL	SC_95_C	CEPH1347.03		TSC-SANGER-SC_95_C-Sep-18-2003-GENOTYPE
230	ss904217	T/T	TSC-CSHL	SC_12_C	CEPH1347.03		TSC-SANGER-SC_12_C-Sep-18-2003-GENOTYPE

Genotype data submitted for	472	samples from	401	individuals	Individual with multiple genotypes submission:	63

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA, PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .