Reference SNP(refSNP) Cluster Report: rs2838471

Reference SNP(refSNP) Cluster Report: rs2838471

refSNP ID: rs2838471
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	100/129
Map to Genome Build:	36.3

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

HGVS Names
NM_001001723.1:c.68-2127A>G
NM_003274.3:c.68-2127A>G
NT_011515.11:g.767181A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10990363 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2838471 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
ss4019187	PERLEGEN\|P00229338	fwd/T	A/G	tgaggtcagatggtcccaggtcaaattcct	cttaggtcagatgacacttttgccactgtt	09/26/01	04/07/04	100	Genomic	unknown
ss4974469	YUSUKE\|IMS-JST145012	fwd/T	A/G	tgaggtcagatggtcccaggtcaaattcct	cttaggtcagatgacacttttgccactgtt	08/12/02	10/10/03	108	Genomic	unknown
ss10990363	BCM_SSAHASNP\|chr21.NT_011515.10_762583	fwd/T	A/G	tgaggtcagatggtcccaggtcaaattcct	cttaggtcagatgacacttttgccactgtt	06/30/03	10/10/03	116	Genomic	unknown
ss15685002	SC_SNP\|NT_011515.10_762583	fwd/T	A/G	tgaggtcagatggtcccaggtcaaattcct	cttaggtcagatgacacttttgccactgtt	11/17/03	11/22/03	120	Genomic	unknown
ss23534948	PERLEGEN\|afd0093955	fwd/T	A/G	tgaggtcagatggtcccaggtcaaattcct	cttaggtcagatgacacttttgccactgtt	08/10/04	09/13/04	123	Genomic	unknown
ss44258090	ABI\|hCV2977972	fwd/T	A/G	tgaggtcagatggtcccaggtcaaattcct	cttaggtcagatgacacttttgccactgtt	07/18/05	07/18/05	126	Genomic	unknown
ss85703951	HGSV\|Cor18517_SNV_20070510.chr21_44274273	fwd/T	A/G	tgaggtcagatggtcccaggtcaaattcct	cttaggtcagatgacacttttgccactgtt	12/06/07	12/10/07	130	Genomic	unknown
ss91856055	BCMHGSC_JDW\|JWB-1503242	fwd/T	A/G	tgaggtcagatggtcccaggtcaaattcct	cttaggtcagatgacacttttgccactgtt	02/26/08	03/02/08	129	Genomic	unknown

Fasta sequence (Legend)

 AATTTCATAA GACTTGATGT GAAGATTTAA GAGTTTATTA AAATAATGGT TGTATATGCT
 GAGAAAATGG TGGTGATTTT TCTTCACATT GTTAATGCAG CGCCTCAGTG GGTTAGAATT
 GGGCCTTCAA ATCTACGCTG GGGCACtgtc ttggtgtgct agggctgccg ccacagagtc
 acacagtctg ggtggcttag cacaaatgcg ctgtgtcaca gctctggaga ccaggtccag
 gcagccacag catgggcctt tgtgtcctca tggggccttc ctgcgttcct tctgtctgtg
 tgaccaaatc ttctctttac acaagtcagt tggattaggg cccatcctga agacctcatt
 ttaactaagc taccttatca actttgaaga ccttatctgc atatggttat attctgaggt
 actggatttt agggcttcaa caggtaggtt tttgtgggac acagttcagc ccataacaGG
 TACTGAGGTC AGATGGTCCC AGGTCAAATT CCT
 R
 CTTAGGTCAG ATGACACTTT TGCCACTGTT GGATGTGCTG ATTGACTGGT CATCTTCTAG
 GTGAACACAG GTTAGAGAGT TAGTCCATGA TGGAATGCGA GAGACATTGC TACTTGGTAG
 TCTCCATTTA GACGAGTCTT ACTGTACGGC AGGGTTCCCA GGGAGAAGAG CTTGGAGCAG
 GTGTTGGAGG CAGTTCCACT

GeneView

GeneView via analysis of contig annotation: TRAPPC10 trafficking protein particle complex 10

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_011515->NM_001001723

function

reference

NT_011515->NM_003274

function

HuRef

NW_001838716->NM_001001723

function

HuRef

NW_001838716->NM_003274

function

Celera

NW_927384->NM_001001723

function

Celera

NW_927384->NM_003274

function

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


reference	NT_011515->NM_001001723->NP_001001723	767181	forward	intron

reference	NT_011515->NM_003274->NP_003265	767181	forward	intron

HuRef	NW_001838716->NM_001001723->NP_001001723	767349	forward	intron

HuRef	NW_001838716->NM_003274->NP_003265	767349	forward	intron

Celera	NW_927384->NM_001001723->NP_001001723	30040606	forward	intron

Celera	NW_927384->NM_003274->NP_003265	30040606	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2838471 maps exactly once on NCBI human chromosome 21

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
21	NW_927384.1	30040606	30555483	plus	A	alt_assembly_1	Celera	Celera	view	513
21	NW_001838716.1	767349	30820337	plus	A	alt_assembly_8	HuRef	HuRef	view	513
21	NT_011515.11	767181	44274273	plus	A	ref_assembly	reference	reference	view	513

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011515.1

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
ss23534948	AFD_EUR_PANEL	European	46	IG	0.565	0.348	0.087	0.655	0.739	0.261

	AFD_AFR_PANEL	African American	46	IG	0.130	0.348	0.522	0.403	0.304	0.696

	AFD_CHN_PANEL	Asian	48	IG	0.625	0.292	0.083	0.403	0.771	0.229

ss4019187	NCBI\|NIHPDR		16	AF					0.688	0.312

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.477+/-0.105	71	50	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .