Reference SNP(refSNP) Cluster Report: rs1805149

Reference SNP(refSNP) Cluster Report: rs1805149

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	89/130
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_001102654.1:c.266G>A
NM_002527.4:c.227G>A
NP_001096124.1:p.Gly89Glu
NP_002518.1:p.Gly76Glu
NT_009759.15:g.5457868G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48421504 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1805149 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
ss2426072	HGBASE\|SNP000063346	fwd/T	A/G	gctccccgagagccggagcggggag	gcccgccaagtcagcattccagcca	11/07/00	10/10/03	89	cDNA	unknown
ss16220922	SC_SNP\|NT_009759.15_5457868	fwd/T	A/G	ctgaggctccccgagagccggagcggggag	gcccgccaagtcagcattccagccggtgat	11/18/03	11/22/03	120	Genomic	unknown
ss48421504	APPLERA_GI\|hCV7499536	rev/B	C/T	atcaccggctggaatgctgacttggcgggc	ctccccgctccggctctcggggagcctcag	09/28/05	11/03/06	126	Genomic	unknown
ss65725922	ILLUMINA\|Human1-rs1805149	fwd/T	A/G	ctgaggctccccgagagccggagcggggag	gcccgccaagtcagcattccagccggtgat	10/10/06	10/10/06	127	Genomic	unknown
ss69099518	PERLEGEN\|PGP04785012	fwd/T	A/G	ctgaggctccccgagagccggagcggggag	gcccgccaagtcagcattccagccggtgat	01/30/07	08/14/07	127	Genomic	unknown
ss74866640	ILLUMINA\|ILMN_Human_1M_rs1805149	fwd/T	A/G	ctgaggctccccgagagccggagcggggag	gcccgccaagtcagcattccagccggtgat	08/28/07	08/29/07	129	Genomic	unknown
ss98341812	CNG\|40001140	fwd/T	A/G	ctgaggctccccgagagccggagcggggag	gcccgccaagtcagcattccagccggtgat	03/31/08	03/31/08	130	Genomic	unknown
ss118537226	ILLUMINA-UK\|NA18507_000007753_NCBI36.1_chr12_5473868	fwd/T	A/G	ctgaggctccccgagagccggagcggggag	gcccgccaagtcagcattccagccggtgat	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 AACACAGACT CAGCTGCCAG AGCCTGCTCT TAACACCTGT GTTTCCTTTT CAGATCTTAC
 AGGTGAACAA GGTGATGTCC ATCTTGTTTT ATGTGATATT TCTCGCTTAT CTCCGTGGCA
 TCCAAGGTAA CAACATGGAT CAAAGGAGTT TGCCAGAAGA CTCGCTCAAT TCCCTCATTA
 TTAAGCTGAT CCAGGCAGAT ATTTTGAAAA ACAAGCTCTC CAAGCAGATG GTGGACGTTA
 AGGAAAATTA CCAGAGCACC CTGCCCAAAG CTGAGGCTCC CCGAGAGCCG GAGCGGGGAG
 R
 GCCCGCCAAG TCAGCATTCC AGCCGGTGAT TGCAATGGAC ACCGAACTGC TGCGACAACA
 GAGACGCTAC AACTCACCGC GGGTCCTGCT GAGCGACAGC ACCCCCTTGG AGCCCCCGCC
 CTTGTATCTC ATGGAGGATT ACGTGGGCAG CCCCGTGGTG GCGAACAGAA CATCACGGCG
 GAAACGGTAC GCGGAGCATA AGAGTCACCG AGGGGAGTAC TCGGTATGTG ACAGTGAGAG
 TCTGTGGGTG ACCGACAAGT CATCGGCCAT CGACATTCGG GGACACCAGG TCACGGTGCT

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_009759.15

dbSNP Blast Analysis

UniGene Cluster ID
99171

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss48421504	HapMap-CEU	European	116	IG			1.000			1.000

	HapMap-HCB	Asian	90	IG	0.022	0.378	0.600		0.211	0.789

	HapMap-JPT	Asian	88	IG	0.023	0.364	0.614		0.205	0.795

	HapMap-YRI	Sub-Saharan African	118	IG		0.356	0.644		0.178	0.822

	AGI_ASP population	multiple	74	IG		0.135	0.865	0.752	0.068	0.932

ss69099518	HapMap-CEU	European	120	GF		0.067	0.933		0.033	0.967

	HapMap-HCB	Asian	90	GF	0.022	0.378	0.600		0.211	0.789

	HapMap-JPT	Asian	90	GF	0.022	0.333	0.644		0.189	0.811

	HapMap-YRI	Sub-Saharan African	120	GF		0.333	0.667		0.167	0.833

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss48421504	1150

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs1805149	1157

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
159	ss48421504	C/C	CSHL-HAPMAP	HapMap-CEU	NA12146	CEPH1334.12	r27_ch12_CEU_illumina:human_1m_beadchip
187	ss48421504	C/C	CSHL-HAPMAP	HapMap-CEU	NA06985	CEPH1341.14	r27_ch12_CEU_illumina:human_1m_beadchip
252	ss48421504	C/C	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	r27_ch12_CEU_illumina:human_1m_beadchip
546	ss48421504	C/C	CSHL-HAPMAP	HapMap-CEU	NA12761	CEPH1447.10	r27_ch12_CEU_illumina:human_1m_beadchip
5143	ss48421504	N/N	CSHL-HAPMAP	HapMap-YRI	NA19193	YOR112.02	r27_ch12_YRI_illumina:human_1m_beadchip
5207	ss48421504	C/T	CSHL-HAPMAP	HapMap-JPT	NA18959	JA18959	r27_ch12_JPT_illumina:human_1m_beadchip
5283	ss48421504	N/N	CSHL-HAPMAP	HapMap-YRI	NA19205	YOR048.01	r27_ch12_YRI_illumina:human_1m_beadchip

Genotype data submitted for	1157	samples from	1157	individuals	Individual with multiple genotypes submission:	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 .