Reference SNP(refSNP) Cluster Report: rs2918150

Reference SNP(refSNP) Cluster Report: rs2918150

refSNP ID: rs2918150
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	101/129
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_174937.3:c.1034+695A>G
NT_008818.15:g.4194621T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss39795917 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2918150 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
ss4116792	SC_JCM\|AC012578.5_47776	fwd/B	C/T	gcatggcacagcaggcccagtcagcaggga	gtgctcactcgctatgcaaggctggtgggg	10/15/01	10/25/06	101	Genomic	unknown
ss10604129	BCM_SSAHASNP\|chr10.NT_008818.14_4183195	fwd/B	C/T	gcatggcacagcaggcccagtcagcaggga	gtgctcactcgctatgcaaggctggtgggg	06/29/03	10/10/03	116	Genomic	unknown
ss12971345	SC_SNP\|NT_008818.14_4183195	fwd/B	C/T	gcatggcacagcaggcccagtcagcaggga	gtgctcactcgctatgcaaggctggtgggg	10/22/03	10/31/03	119	Genomic	unknown
ss16504543	CSHL-HAPMAP\|CSHL-HuAA-200402.chr10.NT_008818.15_4194621	fwd/B	C/T	gcatggcacagcaggcccagtcagcaggga	gtgctcactcgctatgcaaggctggtgggg	02/17/04	03/04/04	120	Genomic	unknown
ss19185661	CSHL-HAPMAP\|CSHL-HuDD-200402.chr10.NT_008818.15_4194621	fwd/B	C/T	gcatggcacagcaggcccagtcagcaggga	gtgctcactcgctatgcaaggctggtgggg	02/20/04	03/04/04	120	Genomic	unknown
ss24546695	PERLEGEN\|afd4118943	fwd/B	C/T	gcatggcacagcaggcccagtcagcaggga	gtgctcactcgctatgcaaggctggtgggg	08/10/04	09/13/04	123	Genomic	unknown
ss39795917	ABI\|hCV3233082	fwd/B	C/T	gcatggcacagcaggcccagtcagcaggga	gtgctcactcgctatgcaaggctggtgggg	07/16/05	11/02/06	126	Genomic	unknown
ss69097187	PERLEGEN\|PGP04118943	fwd/B	C/T	gcatggcacagcaggcccagtcagcaggga	gtgctcactcgctatgcaaggctggtgggg	01/30/07	03/31/08	127	Genomic	unknown

Fasta sequence (Legend)

 GCCTGTGGGG TTTGGCTCTA ACTCCCAGTA GTTAGCATCA GAATCGAGCT AAATTGTAAG
 GGTTGGAGAA TGGGTGGCTG GAAAACAGCA TAATATTAGT ACAAAGAGGT CTCACCCCGA
 GGCACTCCCA GGGTACAGAG GAGCTTTAGC TACAAATGGA AGGCTGGAGG CACCAGGAGC
 CTGCCACCGA CACTGACCAT GGCATAGAAG CCAGGGGTGC CAGTCTGTCC AGATTGGAGC
 CAAGTTCACC CGAATCATCA GAGGACCAGG GCATGGCACA GCAGGCCCAG TCAGCAGGGA
 Y
 GTGCTCACTC GCTATGCAAG GCTGGTGGGG GCCCTGCGCT CCTTAGCCGG CTGCCTTCTG
 TACCTGGCTG GCACATTGAG CTGACACAAG TGGTTGCTAT TTCTGTTCTT TAAATTAGCT
 GTGCCTCCCA GCTGTGTACT GCACTCTCAT CTTCAGGCTT GAAACTTAAT TTTTACTGTA
 ATAACCTTTT ATTCTGCTTC CAAATGACTC CATTATAAAA GGGCATTTTT AAAAACCAAA
 AACTGTAGCT CCCTCGTGGA GGGTGTCTGG AGTGTGGCAT ATTCCGAGAG CAAGCAGCCA

GeneView

GeneView via analysis of contig annotation: TCERG1L transcription elongation regulator 1-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_008818->NM_174937

function

HuRef

NW_001838012->NM_174937

function

Celera

NW_924884->NM_174937

function

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


reference	NT_008818->NM_174937->NP_777597	4194621	reverse	intron

HuRef	NW_001838012->NM_174937->NP_777597	371267	reverse	intron

Celera	NW_924884->NM_174937->NP_777597	43634274	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2918150 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_001838012.1	371267	126535264	plus	C	alt_assembly_8	HuRef	HuRef	view	300
10	NW_924884.1	43634274	126631457	plus	C	alt_assembly_1	Celera	Celera	view	300
10	NT_008818.15	4194621	132850680	plus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_008818 AC067746 AL390203

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC067746.7 NC_000010.9	AC012578.5

UniGene Cluster ID
126575

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24546695	AFD_EUR_PANEL	European	48	IG	0.375	0.375	0.250	0.251	0.562	0.438

	AFD_AFR_PANEL	African American	46	IG	0.565	0.435		0.200	0.783	0.217

	AFD_CHN_PANEL	Asian	48	IG	0.458	0.417	0.125	1.000	0.667	0.333

ss39795917	HapMap-CEU	European	118	IG	0.356	0.475	0.169	1.000	0.593	0.407

	HapMap-HCB	Asian	90	IG	0.533	0.400	0.067	1.000	0.733	0.267

	HapMap-JPT	Asian	90	IG	0.489	0.422	0.089	1.000	0.700	0.300

	HapMap-YRI	Sub-Saharan African	120	IG	0.800	0.200		0.403	0.900	0.100

ss4116792	CHMJ	Asian	74	IG					0.689	0.311

ss69097187	HapMap-CEU	European	120	GF	0.350	0.467	0.183		0.583	0.417

	HapMap-HCB	Asian	90	GF	0.533	0.400	0.067		0.733	0.267

	HapMap-JPT	Asian	90	GF	0.489	0.422	0.089		0.700	0.300

	HapMap-YRI	Sub-Saharan African	120	GF	0.800	0.200			0.900	0.100

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.400+/-0.200	332	260	270	0

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

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .