Reference SNP(refSNP) Cluster Report: rs2026081

Reference SNP(refSNP) Cluster Report: rs2026081

refSNP ID: rs2026081
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	94/129
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_001042758.1:c.1920-678T>C
NM_015326.2:c.1920-678T>C
NT_021877.18:g.143647T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44106315 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2026081 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
ss2934507	TSC-CSHL\|TSC1073232	fwd/T	A/G	cttgacgtctatcatcaaacttgccatact	tatttttaagcattatttcttttctaatta	01/26/01	10/10/03	94	Genomic	unknown
ss23702954	PERLEGEN\|afd1166505	rev/B	C/T	taattagaaaagaaataatgcttaaaaata	agtatggcaagtttgatgatagacgtcaag	08/10/04	09/13/04	123	Genomic	unknown
ss44106315	ABI\|hCV11498162	rev/B	C/T	taattagaaaagaaataatgcttaaaaata	agtatggcaagtttgatgatagacgtcaag	07/18/05	11/03/06	126	Genomic	unknown
ss66149705	AFFY\|SNP_A-2128896	rev/B	C/T	ataatgcttaaaaata	agtatggcaagtttga	10/27/06	08/14/07	127	Genomic	unknown
ss68790535	PERLEGEN\|PGP01166505	rev/B	C/T	taattagaaaagaaataatgcttaaaaata	agtatggcaagtttgatgatagacgtcaag	01/30/07	08/14/07	127	Genomic	unknown
ss76177353	AFFY\|AFFY_6_1M_SNP_A-2128896	rev/B	C/T	ataatgcttaaaaata	agtatggcaagtttga	08/28/07	08/30/07	129	Genomic	unknown

Fasta sequence (Legend)

 AACCTCTGCC TCCCGGGTTT ACGCGATTCT CCTGCCTCAG CCTCCCAAGT AGCTGGGACT
 ACAGACGTGT GCCACCACGC CCAGCTAATT TTTTGTATTA TTAATAGACG GGGTTTCACC
 ATGTTAGCCA GGATGGTCTT GATCTCCTGA CCTCGTGATC TGCCTGCCTC GGCCTCCCAA
 AGTGCTGGGA TTACAGGCGT GAGCCACGCG CCCGACCGCA TCCCCTGCTT TCTACAGTAA
 CTTCTTTGGT GTTTCCAAAG ATCTTCATGC CTTGACGTCT ATCATCAAAC TTGCCATACT
 R
 TATTTTTAAG CATTATTTCT TTTCTAATTA TATAATAATT CCAGTAATTG TAGAAAATGT
 ATCATACATT TTTTAGAATA CATACATGTA TTCTAAATAT TTTATGTTAT CCATTCCCCC
 TAGTAAGTAG AATGTGAGCT TTCTGTCTCT CTATAAAGAG AAAATAACTT GCCCAATCAA
 CTTTCCAAGG AGCAAAATAT GAAAATATAT TTTGTGACCA ACCTATGAAA AAAATGCACA
 TGAAAGTAAT CTAAAAAAGT AAAAGGGGTC TACGAATGCA ATCTATCTTT ATTTTTGTGT

GeneView

GeneView via analysis of contig annotation: SRGAP2 SLIT-ROBO Rho GTPase activating protein 2

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_021877->NM_001042758

function

reference

NT_021877->NM_015326

function

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


reference	NT_021877->NM_001042758->NP_001036223	143647	forward	intron

reference	NT_021877->NM_015326->NP_056141	143647	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2026081 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838536.1	56915	177324111	minus	T	alt_assembly_8	HuRef	HuRef	view	300
1	NW_926794.1	43071	179877311	minus	T	alt_assembly_1	Celera	Celera	view	300
1	NT_021877.18	143647	204692491	minus	T	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000001.8

dbSNP Blast Analysis
GenBank HTGS Finished:
AL161736.33

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss23702954	AFD_EUR_PANEL	European	48	IG	0.750	0.167	0.083	0.100	0.833	0.167

	AFD_AFR_PANEL	African American	46	IG	0.609	0.348	0.043	1.000	0.783	0.217

	AFD_CHN_PANEL	Asian	48	IG	0.958	0.042		1.000	0.979	0.021

ss44106315	HapMap-CEU	European	120	IG	0.717	0.267	0.017	0.752	0.850	0.150

	HapMap-HCB	Asian	90	IG	0.867	0.133		0.655	0.933	0.067

	HapMap-JPT	Asian	90	IG	0.889	0.089	0.022	0.100	0.933	0.067

	HapMap-YRI	Sub-Saharan African	120	IG	0.650	0.350		0.150	0.825	0.175

ss66149705	HapMap-CEU	European	118	GF	0.712	0.271	0.017		0.847	0.153

	HapMap-HCB	Asian	90	GF	0.867	0.133			0.933	0.067

	HapMap-JPT	Asian	90	GF	0.889	0.089	0.022		0.933	0.067

	HapMap-YRI	Sub-Saharan African	120	GF	0.650	0.350			0.825	0.175

ss68790535	HapMap-CEU	European	120	GF	0.700	0.283	0.017		0.842	0.158

	HapMap-HCB	Asian	90	GF	0.867	0.133			0.933	0.067

	HapMap-JPT	Asian	90	GF	0.889	0.089	0.022		0.933	0.067

	HapMap-YRI	Sub-Saharan African	120	GF	0.650	0.350			0.825	0.175

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss23702954	71
ss44106315	269
ss66149705	268
ss68790535	269

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs2026081	332

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
362	ss44106315	T/T	CSHL-HAPMAP	HapMap-CEU	NA11994	CEPH1362.15	r23_ch1_CEU_perlegen:genotyping_1.0.0	1667548
362	ss66149705	T/T	CSHL-HAPMAP	HapMap-CEU	NA11994	CEPH1362.15	chr1-HapMap-CEU
362	ss68790535	C/T	CSHL-HAPMAP	HapMap-CEU	NA11994	CEPH1362.15	chr1-HapMap-CEU

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

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Revised: May 25, 2006 1:38 PM .