Reference SNP(refSNP) Cluster Report: rs2978083

Reference SNP(refSNP) Cluster Report: rs2978083

refSNP ID: rs2978083
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:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_015850.3:c.92-1437G>A
NM_023105.2:c.92-2950G>A
NM_023106.2:c.92-2950G>A
NM_023107.2:c.92-2950G>A
NM_023108.2:c.92-2950G>A
NM_023110.2:c.92-1437G>A
NM_023111.2:c.92-1437G>A
NT_007995.14:g.8609292C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss4192130 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2978083 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
ss4192130	SC_JCM\|AF214633.3_9859	fwd/T	A/G	cgtagtaggtgctggggatttaaaggtacc	atgacacatcaccgcactcaggttcagaaa	10/15/01	10/25/06	101	Genomic	unknown
ss24462637	PERLEGEN\|afd4220622	rev/B	C/T	tttctgaacctgagtgcggtgatgtgtcat	ggtacctttaaatccccagcacctactacg	08/10/04	09/13/04	123	Genomic	unknown
ss67286512	ILLUMINA\|HumanHap550v1.1_rs2978083	fwd/T	A/G	cgtagtaggtgctggggatttaaaggtacc	atgacacatcaccgcactcaggttcagaaa	11/14/06	11/14/06	127	Genomic	unknown
ss67689430	ILLUMINA\|HumanHap650Yv1.0_rs2978083	fwd/T	A/G	cgtagtaggtgctggggatttaaaggtacc	atgacacatcaccgcactcaggttcagaaa	11/14/06	11/14/06	127	Genomic	unknown
ss68216400	ILLUMINA\|HumanHap250Sv1.0_rs2978083	fwd/T	A/G	cgtagtaggtgctggggatttaaaggtacc	atgacacatcaccgcactcaggttcagaaa	12/06/06	12/07/06	127	Genomic	unknown
ss69047052	PERLEGEN\|PGP04220622	rev/B	C/T	tttctgaacctgagtgcggtgatgtgtcat	ggtacctttaaatccccagcacctactacg	01/30/07	03/31/08	127	Genomic	unknown
ss70765066	ILLUMINA\|HumanHap550v3.0__rs2978083	rev/B	C/T	tttctgaacctgagtgcggtgatgtgtcat	ggtacctttaaatccccagcacctactacg	04/20/07	03/30/08	130	Genomic	unknown
ss71339530	ILLUMINA\|HumanHap650Yv3.0_rs2978083	fwd/T	A/G	cgtagtaggtgctggggatttaaaggtacc	atgacacatcaccgcactcaggttcagaaa	04/23/07	04/23/07	127	Genomic	unknown
ss75574938	ILLUMINA\|ILMN_Human_1M_rs2978083	fwd/T	A/G	cgtagtaggtgctggggatttaaaggtacc	atgacacatcaccgcactcaggttcagaaa	08/28/07	08/29/07	129	Genomic	unknown
ss84135505	KRIBB_YJKIM\|KHS643024	fwd/T	A/G	cgtagtaggtgctggggatttaaaggtacc	atgacacatcaccgcactcaggttcagaaa	12/04/07	12/06/07	130	Genomic	unknown

Fasta sequence (Legend)

 AAGGTTTCTA GCGGAAGCCT GTTGAGCACT TGAGGAAGAC CGTGTTTCAA ATAAGGGGGA
 GTGAAAGAGA AAAGGGAGAG TAGAAAGGAA GGCAGTGAAG AGCCAGAGTG ACTGCACGTG
 TGGTatttat tgagcaagca tttcttgagc aactcctggg cgccaggcat cgtagtaggt
 gctggggatT TAAAGGTACC
 R
 ATGACACATC ACCGCACTCA GGTTCAGAAA GAGGACTGCC CTTCAGTGTG ACAGGTGCCA
 GGAGGGGGAG GGCACCTAAC CCAGACTGGG AGTCAGCACC GCCCTGGAGG AGAAGTCACC
 AGCTAGGCTG AGACAGAAGA GTGAGTAGTG AGAGCTGGAC AGAAAAAAAT CAGGGGCCCT
 GTGGCCACTG GGGCAGCCGT

GeneView

GeneView via analysis of contig annotation: FGFR1 fibroblast growth factor receptor 1

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_007995->NM_015850

function

reference

NT_007995->NM_023105

function

reference

NT_007995->NM_023106

function

reference

NT_007995->NM_023107

function

reference

NT_007995->NM_023108

function

reference

NT_007995->NM_023110

function

reference

NT_007995->NM_023111

function

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


reference	NT_007995->NM_015850->NP_056934	8609292	reverse	intron

reference	NT_007995->NM_023105->NP_075593	8609292	reverse	intron

reference	NT_007995->NM_023106->NP_075594	8609292	reverse	intron

reference	NT_007995->NM_023107->NP_075595	8609292	reverse	intron

reference	NT_007995->NM_023108->NP_075596	8609292	reverse	intron

reference	NT_007995->NM_023110->NP_075598	8609292	reverse	intron

reference	NT_007995->NM_023111->NP_075599	8609292	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2978083 maps exactly once on NCBI human chromosome 8

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
8	NW_001839128.2	488114	36822892	plus	G	alt_assembly_8	HuRef	HuRef	view	200
8	NW_923907.1	25809723	37241885	minus	C	alt_assembly_1	Celera	Celera	view	200
8	NT_007995.14	8609292	38408060	minus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000008.9 AC011237 AC087623 AC090129

dbSNP Blast Analysis
GenBank HTGS Draft:
AF214633.4

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24462637	AFD_EUR_PANEL	European	48	IG		0.208	0.792	0.584	0.104	0.896

	AFD_AFR_PANEL	African American	46	IG			1.000			1.000

	AFD_CHN_PANEL	Asian	48	IG			1.000			1.000

ss4192130	HapMap-CEU	European	116	IG	0.017	0.121	0.862	0.251	0.078	0.922

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	90	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG			1.000			1.000

ss69047052	HapMap-CEU	European	120	GF	0.017	0.150	0.833		0.092	0.908

	HapMap-HCB	Asian	90	GF			1.000			1.000

	HapMap-JPT	Asian	90	GF			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF			1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.050+/-0.150	332	260	270	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 .