Reference SNP(refSNP) Cluster Report: rs2229540

Reference SNP(refSNP) Cluster Report: rs2229540

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	98/130
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_006066.2:c.155A>G
NM_153326.1:c.155A>G
NP_006057.1:p.Asn52Ser
NP_697021.1:p.Asn52Ser
NT_032977.8:g.16004229A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48418114 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2229540 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
ss3176571	WICVAR\|WI-18696	fwd/T	A/G	gccacattgattgtgctgctatctacggca	tgagcctgagattggggaggccctgaagga	06/28/01	10/10/03	98	cDNA	unknown
ss16242921	CGAP-GAI\|1483135	fwd/T	A/G	gccacattgattgtgctgctatctacggca	tgagcctgagattggggaggccctgaagga	11/18/03	11/22/03	126	cDNA	unknown
ss48418114	APPLERA_GI\|hCV16172465	rev/B	C/T	tccttcagggcctccccaatctcaggctca	tgccgtagatagcagcacaatcaatgtggc	09/28/05	11/03/06	126	Genomic	unknown
ss68765032	PERLEGEN\|PGP04768715	fwd/T	A/G	gccacattgattgtgctgctatctacggca	tgagcctgagattggggaggccctgaagga	01/30/07	08/14/07	127	Genomic	unknown
ss74908232	ILLUMINA\|ILMN_Human_1M_rs2229540	fwd/T	A/G	gccacattgattgtgctgctatctacggca	tgagcctgagattggggaggccctgaagga	08/28/07	08/29/07	129	Genomic	unknown
ss77626976	HGSV\|Cor12156_SNV_20070510.chr1_45701404	fwd/T	A/G	gccacattgattgtgctgctatctacggca	tgagcctgagattggggaggccctgaagga	10/09/07	10/13/07	129	Genomic	unknown
ss86341956	CANCER-GENOME\|12643	fwd/T	A/G	gccacattgattgtgctgctatctacggca	tgagcctgagattggggaggccctgaagga	01/25/08	01/25/08	129	Genomic	unknown
ss108166219	1000GENOMES\|CEU.trio.12.15.2008_56538_chr1_45804898	fwd/T	A/G	gccacattgattgtgctgctatctacggca	tgagcctgagattggggaggccctgaagga	12/15/08	12/15/08	130	Genomic	unknown

Fasta sequence (Legend)

 GCTGGTCTCG AACTCCTGAC CTCAGGGGAT CTGCCCACCT CAGCCTCCCA AAGTGCTGGG
 ATTACAGGCG TGAGCCACCG CGCCCAGTTC ATCTTCCATC TTTTCACCTC CACTGCATAG
 ATGTGCCTGT TATATTTCTG AGCCCCCTTC CCCCAGCATT GACCTTGGGG TGGTGACAGT
 AGAAGGCTGA AACCAACATA GCTGAAACCT CTGCTTCTCT CACCTGGCAG GTAAAAGCAG
 CTGTTAAGTA TGCCCTTAGC GTAGGCTACC GCCACATTGA TTGTGCTGCT ATCTACGGCA
 R
 TGAGCCTGAG ATTGGGGAGG CCCTGAAGGA GGACGTGGGA CCAGGCAAGG TAAGGACTGG
 GGTTGTAAAT AGAGGTGGGA TAAGAGAACT TAGAAGCTGA AGCTAGGGCT GGGGCCCAGC
 TGGAGGGAAT CTGGCATCAG CTTCCTTCCA GTTCCTCTCC CAGAGTTGAG GGTGGGTGAG
 ACCACGTGCT CATGGCTCTT CTCACTGTGG GCCCTGCCCC CTGCACTAGG CGGTGCCTCG
 GGAGGAGCTG TTTGTGACAT CCAAGCTGTG GAACACCAAG CACCACCCCG AGGATGTGGA

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
NM_006066 BE903027

dbSNP Blast Analysis

UniGene Cluster ID
474584

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	HWP	A	G
ss3176571	MITOGPOP6	multiple	52	IG	0.962	0.038	1.000	0.981	0.019

ss48418114	HapMap-CEU	European	114	IG	0.912	0.088		0.956	0.044

	HapMap-HCB	Asian	88	IG	1.000			1.000

	HapMap-JPT	Asian	86	IG	1.000			1.000

	HapMap-YRI	Sub-Saharan African	116	IG	1.000			1.000

	AGI_ASP population	multiple	78	IG	0.923	0.077	1.000	0.962	0.038

ss68765032	HapMap-CEU	European	120	GF	0.950	0.050		0.975	0.025

	HapMap-HCB	Asian	90	GF	0.889	0.111		0.944	0.056

	HapMap-JPT	Asian	90	GF	0.933	0.067		0.967	0.033

	HapMap-YRI	Sub-Saharan African	120	GF	0.967	0.033		0.983	0.017

Concordant Genotype	Total Sample	A/A	A/G
ss3176571	26	25	1
ss48418114	807

RefSNP Genotype Summary	Total Individual	A/A	A/G
rs2229540	839	25	1

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
151	ss48418114	T/T	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	r27_ch1_CEU_illumina:human_1m_beadchip
159	ss48418114	T/T	CSHL-HAPMAP	HapMap-CEU	NA12146	CEPH1334.12	r27_ch1_CEU_illumina:human_1m_beadchip
360	ss48418114	C/T	CSHL-HAPMAP	HapMap-CEU	NA11992	CEPH1362.13	r27_ch1_CEU_illumina:human_1m_beadchip
576	ss48418114	C/T	CSHL-HAPMAP	HapMap-CEU	NA12812	CEPH1454.12	r27_ch1_CEU_illumina:human_1m_beadchip
637	ss48418114	C/T	CSHL-HAPMAP	HapMap-CEU	NA12892	CEPH1463.16	r27_ch1_CEU_illumina:human_1m_beadchip
5139	ss48418114	T/T	CSHL-HAPMAP	HapMap-YRI	NA19100	YOR105.01	r27_ch1_YRI_bcm:genotype_0002
5150	ss48418114	T/T	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	r27_ch1_CHB_bcm:genotype_0002
5169	ss48418114	T/T	CSHL-HAPMAP	HapMap-HCB	NA18564	CH18564	r27_ch1_CHB_bcm:genotype_0002
5174	ss48418114	T/T	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r27_ch1_CHB_bcm:genotype_0002
5180	ss48418114	T/T	CSHL-HAPMAP	HapMap-HCB	NA18623	CH18623	r27_ch1_CHB_bcm:genotype_0002
5192	ss48418114	T/T	CSHL-HAPMAP	HapMap-HCB	NA18637	CH18637	r27_ch1_CHB_bcm:genotype_0002
5201	ss48418114	T/T	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	r27_ch1_JPT_bcm:genotype_0002
5230	ss48418114	T/T	CSHL-HAPMAP	HapMap-JPT	NA18997	JA18997	r27_ch1_JPT_bcm:genotype_0002
5232	ss48418114	T/T	CSHL-HAPMAP	HapMap-JPT	NA19000	JA19000	r27_ch1_JPT_bcm:genotype_0002
5252	ss48418114	T/T	CSHL-HAPMAP	HapMap-YRI	NA18522	YOR016.03	r27_ch1_YRI_bcm:genotype_0002
5294	ss48418114	T/T	CSHL-HAPMAP	HapMap-YRI	NA19160	YOR056.03	r27_ch1_YRI_bcm:genotype_0002

Genotype data submitted for	849	samples from	839	individuals	Individual with multiple genotypes submission:	10

Validation Summary:

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

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Revised: May 25, 2006 1:38 PM .