Reference SNP(refSNP) Cluster Report: rs1261116

Reference SNP(refSNP) Cluster Report: rs1261116

refSNP ID: rs1261116
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
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_001083962.1:c.550-2663T>C
NM_003199.2:c.550-2663T>C
NT_025028.13:g.740414A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44074491 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1261116 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
ss1935629	KWOK\|OVLP-000925-736653	fwd/T	A/G	gtcacagaaacatcactcttatttttcacc	tttgatagggtacttttttttagaatggtg	10/06/00	10/10/03	87	Genomic	99 %
ss2667288	SC_JCM\|AC073440.9_117795	fwd/T	A/G	gtcacagaaacatcactcttatttttcacc	tttgatagggtacttttttttagaatggtg	11/03/00	10/10/03	89	Genomic	unknown
ss44074491	ABI\|hCV8923320	fwd/T	A/G	gtcacagaaacatcactcttatttttcacc	tttgatagggtacttttttttagaatggtg	07/18/05	11/03/06	126	Genomic	unknown
ss81389635	HGSV\|Cor18507_SNV_20070510.chr18_51100548	fwd/T	A/G	gtcacagaaacatcactcttatttttcacc	tttgatagggtacttttttttagaatggtg	11/26/07	11/29/07	130	Genomic	unknown
ss83145037	HGSV\|Cor19240_SNV_20070510.chr18_51100548	fwd/T	A/G	gtcacagaaacatcactcttatttttcacc	tttgatagggtacttttttttagaatggtg	11/30/07	12/04/07	130	Genomic	unknown
ss85260651	HGSV\|Cor18517_SNV_20070510.chr18_51100548	fwd/T	A/G	gtcacagaaacatcactcttatttttcacc	tttgatagggtacttttttttagaatggtg	12/06/07	12/08/07	130	Genomic	unknown

Fasta sequence (Legend)

 TGTTTATAGT TTTTTATACA GACAATTTCT ACATATTTTA TACATTTTCT TTATATCATA
 ATTTACAAAT CAGATACAAT GTTATTCATC TTCCATTTAG ATACTTTATC ATTCTTACCT
 CAAAAGTTAT TTTCAAGGTA AGATCTCTAT ATTTTTGTTT ATATAAATAA ATAAATATCA
 CATATAACTA TACTTTTTTA AAGAAGGGAA CCAACAAATT TTAGTTCAAC CTCCCACATT
 TCAAATATAA GAAAACTGAA TAATGAAATG GTCACAGAAA CATCACTCTT ATTTTTCACC
 R
 TTTGATAGGG TACTTTTTTT TAGAATGGTG GCGGAGACAT AGATGGTATT TATGAAAACA
 CCATGATCAT AATTTTCACA GTTCAGTTTA TCTCTAATGG TTTAATTTTT CATAACCTGG
 ATGACCAGTG AACTGCTTCA TTACTTTTAC TTCAGTCAAC TCTTTTGCCA ATTTCTCAAT
 CAAGCTTTCA AAGTATGGGT TTCAATAAGG TATTTAATAC TGACATTAAA TTCAATAAGA
 AAAGCTCATA CCCATTCAGT TTTTAGTATT ATTATTCTAA GTATATAGAA AGTTTAACAA

GeneView

GeneView via analysis of contig annotation: TCF4 transcription factor 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_025028->NM_001083962

function

reference

NT_025028->NM_003199

function

HuRef

NW_001838469->NM_001083962

function

HuRef

NW_001838469->NM_003199

function

Celera

NW_927106->NM_001083962

function

Celera

NW_927106->NM_003199

function

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


reference	NT_025028->NM_001083962->NP_001077431	740414	reverse	intron

reference	NT_025028->NM_003199->NP_003190	740414	reverse	intron

HuRef	NW_001838469->NM_001083962->NP_001077431	742516	reverse	intron

HuRef	NW_001838469->NM_003199->NP_003190	742516	reverse	intron

Celera	NW_927106->NM_001083962->NP_001077431	8260501	reverse	intron

Celera	NW_927106->NM_003199->NP_003190	8260501	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1261116 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_001838469.1	742516	49659167	plus	A	alt_assembly_8	HuRef	HuRef	view	300
18	NW_927106.1	8260501	49666918	plus	A	alt_assembly_1	Celera	Celera	view	300
18	NT_025028.13	740414	51100548	plus	A	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
AP001493.2 AP001399 AP001493 AP001544 AP001548 AP001548.2

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC091103.4 AC091111.5 NC_000018.8	AC073440.12 AC090405.2 AP001399.3 AP001493.2 AP001544.3 AP001548.2 AP002896.1

Population Diversity

	Sample Ascertainment				Genotypes	Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	HWP	A	G
ss44074491	AoD_African_American		90	AF		0.760	0.240

	AoD_Caucasian		92	AF		0.930	0.070

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.261+/-0.250	0	0	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .