Reference SNP(refSNP) Cluster Report: rs3800019

Reference SNP(refSNP) Cluster Report: rs3800019

refSNP ID: rs3800019
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/129
Map to Genome Build:	36.3

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

HGVS Names
NM_016277.3:c.241+3486C>T
NM_183227.1:c.241+3486C>T
NT_007592.14:g.47927171G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44765616 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3800019 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
ss2102532	TSC-CSHL\|TSC0818533	fwd/B	C/T	attgaagtagcttgcttatttacaaactta	accagttatataaaatcgatatacttgaga	06/14/01	10/25/06	108	Genomic	unknown
ss4986402	YUSUKE\|IMS-JST158408	fwd/B	C/T	attgaagtagcttgcttatttacaaactta	accagttatataaaatcgatatacttgaga	08/12/02	10/10/03	107	Genomic	unknown
ss5703986	SC_JCM\|NT_007592.10_47871720	rev/T	A/G	tctcaagtatatcgattttatataactggt	taagtttgtaaataagcaagctacttcaat	01/10/03	10/10/03	111	Genomic	unknown
ss44765616	ABI\|hCV8301542	rev/T	A/G	tctcaagtatatcgattttatataactggt	taagtttgtaaataagcaagctacttcaat	07/19/05	11/03/06	126	Genomic	unknown
ss65792514	ILLUMINA\|Human1-rs3800019	fwd/T	C/T	attgaagtagcttgcttatttacaaactta	accagttatataaaatcgatatacttgaga	10/10/06	10/10/06	127	Genomic	unknown
ss68978171	PERLEGEN\|PGP13227099	rev/T	A/G	tctcaagtatatcgattttatataactggt	taagtttgtaaataagcaagctacttcaat	01/30/07	03/31/08	127	Genomic	unknown
ss74894720	ILLUMINA\|ILMN_Human_1M_rs3800019	fwd/B	C/T	attgaagtagcttgcttatttacaaactta	accagttatataaaatcgatatacttgaga	08/28/07	08/29/07	129	Genomic	unknown
ss84654648	HGSV\|Cor18517_SNV_20070510.chr6_57176899	rev/T	A/G	tctcaagtatatcgattttatataactggt	taagtttgtaaataagcaagctacttcaat	12/06/07	12/07/07	130	Genomic	unknown
ss93467698	BCMHGSC_JDW\|JWB-2145804	rev/T	A/G	tctcaagtatatcgattttatataactggt	taagtttgtaaataagcaagctacttcaat	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 ATGGAAATTC TTCTGACTTC TTCATGGAAG TCTTCTTTAA TGTGTCACTT TACCCAATTT
 GAAAGGGAAC CTATGTTTGT GTGTCCTGGA TTATCAGAGA AGCAGTACTT GAAAATAGAA
 TAGATATATT GAATAGCAGT ATACCAGTAT GTGTCTCTTG AAGAAATCTA TATATATGAA
 AGTTCCAAGT GACAGTGTTA ATGAACTTTT AGGTACAGTA TCATATAAAC ACATAATTTC
 TTCTTTTAGA CAGGATTTAC CACTGATTTT ATTGAAGTAG CTTGCTTATT TACAAACTTA
 Y
 ACCAGTTATA TAAAATCGAT ATACTTGAGA AATTGGGTGA ATTCATGTAA CTTTTGAATA
 TATAGCTTAT TTTTTTCGCT TTTGAAAATG TAGGATTTAT TGTAATAATG ACAACTAAGG
 TTTCATGATT GTACTAACAT ACAAATGACC AAAGAAGTTG CCTTTCTAAA TTGGTACCAA
 GGAAACTTGA CTTCCACTGC CTGCTCTAAA ACATATTTTG GTTTCTTGCC ACCACTACTT
 ACCACTCTAT TTACTGTGTA CTTTAAGGCT TCCCGTCCAC AGTAGCTTTG GTTATTCTCT

GeneView

GeneView via analysis of contig annotation: RAB23 RAB23, member RAS oncogene family

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_007592->NM_016277

function

reference

NT_007592->NM_183227

function

HuRef

NW_001838981->NM_016277

function

HuRef

NW_001838981->NM_183227

function

Celera

NW_923073->NM_016277

function

Celera

NW_923073->NM_183227

function

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


reference	NT_007592->NM_016277->NP_057361	47927171	reverse	intron

reference	NT_007592->NM_183227->NP_899050	47927171	reverse	intron

HuRef	NW_001838981->NM_016277->NP_057361	364901	forward	intron

HuRef	NW_001838981->NM_183227->NP_899050	364901	forward	intron

Celera	NW_923073->NM_016277->NP_057361	30196360	reverse	intron

Celera	NW_923073->NM_183227->NP_899050	30196360	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3800019 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838981.2	364901	56902997	plus	C	alt_assembly_8	HuRef	HuRef	view	300
6	NT_007592.14	47927171	57176899	minus	G	ref_assembly	reference	reference	view	300
6	NW_923073.1	30196360	58732039	minus	G	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007592.10

dbSNP Blast Analysis
GenBank HTGS Finished:
AL031321.1 NC_000006.10

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss44765616	HapMap-CEU	European	116	IG	0.810	0.172	0.017	0.655	0.897	0.103

	HapMap-HCB	Asian	90	IG	0.800	0.178	0.022	0.527	0.889	0.111

	HapMap-JPT	Asian	88	IG	0.818	0.159	0.023	0.403	0.898	0.102

	HapMap-YRI	Sub-Saharan African	118	IG	0.356	0.508	0.136	0.527	0.610	0.390

	AoD_African_American		90	AF					0.600	0.400

	AoD_Caucasian		92	AF					0.870	0.130

	AoD_Chinese		90	AF					0.760	0.240

	AoD_Japanese		90	AF					0.880	0.120

ss68978171	HapMap-CEU	European	120	GF	0.783	0.200	0.017		0.883	0.117

	HapMap-HCB	Asian	88	GF	0.818	0.159	0.023		0.898	0.102

	HapMap-JPT	Asian	90	GF	0.822	0.156	0.022		0.900	0.100

	HapMap-YRI	Sub-Saharan African	120	GF	0.367	0.500	0.133		0.617	0.383

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss44765616	267
ss68978171	267

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs3800019	270

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
151	ss44765616	A/G	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	r23_ch6_CEU_illumina:infinium_genotyping_1.0.0	496280
151	ss68978171	G/G	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	chr6-HapMap-CEU
262	ss44765616	G/G	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	r23_ch6_CEU_illumina:infinium_genotyping_1.0.0	496280
262	ss68978171	A/G	CSHL-HAPMAP	HapMap-CEU	NA11829	CEPH1350.10	chr6-HapMap-CEU
5146	ss44765616	A/G	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	r23_ch6_YRI_illumina:infinium_genotyping_1.0.0	496280
5146	ss68978171	G/G	CSHL-HAPMAP	HapMap-YRI	NA19238	YOR117.02	chr6-HapMap-YRI

Genotype data submitted for	270	samples from	270	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, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .