Reference SNP(refSNP) Cluster Report: rs916146

Reference SNP(refSNP) Cluster Report: rs916146

refSNP ID: rs916146
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
Map to Genome Build:	36.3

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

HGVS Names
NM_003367.2:c.728-1139C>A
NM_207291.1:c.527-1139C>A
NT_011109.15:g.8036680C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44157317 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs916146 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
ss1351540	TSC-CSHL\|TSC0200998	fwd/T	A/C	gtgtgagggtaacgggcaggctgtggccca	ccctccttctcaggctcactggacccctga	09/06/00	10/25/06	86	Genomic	95 %
ss44157317	ABI\|hCV7612706	fwd/T	A/C	gtgtgagggtaacgggcaggctgtggccca	ccctccttctcaggctcactggacccctga	07/18/05	11/03/06	126	Genomic	unknown
ss75207919	ILLUMINA\|ILMN_Human_1M_rs916146	fwd/T	A/C	gtgtgagggtaacgggcaggctgtggccca	ccctccttctcaggctcactggacccctga	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 ATAGCAAGCA CTGATCTTGG GCTATTGGTT TTGGAGGAAA GAGGGAGCAC AAGGATGGAA
 GGGGCCAGGG AAGAGAGGTC ACGGTGGGAG AAGGAGAGTC CGCATCCATC GGAGGGTTTG
 TCACTCAGGC CTGAGTGGGA GGCACTGGAG GCAGGGAGAG GCCAGTCAGC AGCATGCGGC
 CACAGCCCAG AGAAGCCAGA GGGGTTTGCT GGTGGGTGGG CCCCAGCCTT TTCAAGGGAA
 CGGCAGGTCT GGGGAGCTGC CGATCTCGGG GTGTGAGGGT AACGGGCAGG CTGTGGCCCA
 M
 CCCTCCTTCT CAGGCTCACT GGACCCCTGA CCGGTTTCAT CACCATTATC CAAGGCTTTG
 AAAAGACCCC CTGGCCTTCC TGCCACATGT GCCCTAGCTA TAGGGCTTCG TTCCCCTCCA
 CAAATGGTGC AGACAGCATG AGCCACCCTG GCAGGGGGCT GGGGGTCCGT GGGGTAGGAG
 TTGGGGGTAG CTGAGCGTTC TTTCCTGTCC CCACGGTGCC TGGTGCTGGG GCTTGGCAGC
 CAGGGTTGGG ACAGCCTGGC TTTAGCAGGT CCTGAGTCAG GGGTCTCAGG CTCCGCAGCA

GeneView

GeneView via analysis of contig annotation: USF2 upstream transcription factor 2, c-fos interacting

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_011109->NM_003367

function

reference

NT_011109->NM_207291

function

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


reference	NT_011109->NM_003367->NP_003358	8036680	forward	intron

reference	NT_011109->NM_207291->NP_997174	8036680	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs916146 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838494.1	889149	32277092	plus	C	alt_assembly_8	HuRef	HuRef	view	300
19	NW_927206.1	8053468	32481900	plus	A	alt_assembly_1	Celera	Celera	view	300
19	NT_011109.15	8036680	40460302	plus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
AD000684.1 Y07661.1

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss1351540	CEPH		184	AF						1.000

ss44157317	HapMap-CEU	European	120	IG			1.000			1.000

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.417	0.500	1.000	0.292	0.708

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.153+/-0.231	270	210	0	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

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Revised: May 25, 2006 1:38 PM .