Reference SNP(refSNP) Cluster Report: rs2228220

Reference SNP(refSNP) Cluster Report: rs2228220

refSNP ID: rs2228220
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	98/129
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_002114.2:c.3221A>G
NP_002105.2:p.N1074S
NT_007592.14:g.2981506A>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48428064 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2228220 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
ss3172881	WIAF-CSNP\|WIAF-13016	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	06/19/01	04/07/04	98	cDNA	unknown
ss4986885	YUSUKE\|IMS-JST158952	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	08/12/02	10/10/03	108	Genomic	unknown
ss23756835	PERLEGEN\|afd1476872	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	08/10/04	09/13/04	123	Genomic	unknown
ss48428064	APPLERA_GI\|hCV16170804	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	09/28/05	11/03/06	126	Genomic	unknown
ss66136525	AFFY\|SNP_A-2090013	rev/B	C/T	acttcttatggtaaca	tatgtttaggcaaact	10/27/06	08/14/07	127	Genomic	unknown
ss66644071	ILLUMINA\|HumanHap300v1.1_rs2228220	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	11/09/06	11/09/06	127	Genomic	unknown
ss67235489	ILLUMINA\|HumanHap550v1.1_rs2228220	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	11/14/06	11/14/06	127	Genomic	unknown
ss67631583	ILLUMINA\|HumanHap650Yv1.0_rs2228220	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	11/14/06	11/14/06	127	Genomic	unknown
ss68965490	PERLEGEN\|PGP01476872	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	01/30/07	08/14/07	127	Genomic	unknown
ss70713831	ILLUMINA\|HumanHap550v3.0__rs2228220	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	04/20/07	03/30/08	130	Genomic	unknown
ss71281511	ILLUMINA\|HumanHap650Yv3.0_rs2228220	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	04/23/07	04/23/07	127	Genomic	unknown
ss75522160	ILLUMINA\|ILMN_Human_1M_rs2228220	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	08/28/07	08/29/07	129	Genomic	unknown
ss76149303	AFFY\|AFFY_6_1M_SNP_A-2090013	rev/B	C/T	acttcttatggtaaca	tatgtttaggcaaact	08/28/07	08/30/07	129	Genomic	unknown
ss76874291	CGM_KYOTO\|495396	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	09/12/07	09/12/07	129	cDNA	unknown
ss79121672	ILLUMINA\|HumanHap300v2.0_rs2228220	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	04/18/07	11/18/07	130	Genomic	unknown
ss84001655	KRIBB_YJKIM\|KHS598144	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	12/04/07	12/06/07	130	Genomic	unknown
ss109761680	1000GENOMES\|CEU.trio.12.15.2008_1451416_chr6_12231235	fwd/T	A/G	tgggctgtaatcccagtttgcctaaacata	tgttaccataagaagtgaccagcagcataa	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 TTGAAAATCA TAAGAAATTT TACTGTTCTG AGTTACATGG ACCAAAAACA AAGGTAGCCA
 TGAGAGAACC TGAGCACAGC CCTGTGCCCG GCGGTCTGCA GCCTCAGATT CTACACTACA
 GAGTCGCTGG GTCCTCCGGC ATCTGGGAAC AGACGCCCCA GATAAGAAAA AGGAGGAAAA
 TGAAAAGTGT TGGGGATGAT GAAGAACTTC AGCAAAATGA AAGTGGAACA TCTCCAAAAA
 GTTCTGAAGG CCTTCAGTTT CAGAATGCTC TGGGCTGTAA TCCCAGTTTG CCTAAACATA
 R
 TGTTACCATA AGAAGTGACC AGCAGCATAA AAATATACAG TTGCAAAACT CCCATATTCA
 CCTTGTTGCC AGGGGCCCTG AGCAGACCAT GGATCCCAAG CTGTCGACCA TCATGGAACA
 ACAGATAAGT TCAGCAGCCC AGGACAAGAT AGAACTGCAG AGACACGGAA CTGGAATCTC
 TGTCATCCAG CACACCAACT CCCTGAGCAG GCCCAACTCA TTTGACAAGC CTGAGCCTTT
 TGAAAGAGCC TCCCCAGTTT CTTTCCAGGA GCTGAATAGA ACGGGGAAGT CCGGGTCTCT

GeneView

GeneView via analysis of contig annotation: HIVEP1 human immunodeficiency virus type I enhancer binding protein 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_007592->NM_002114

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_007592->NM_002114->NP_002105	2981507	forward	3400	missense	G	Ser [S]	2	1074
					contig reference	A	Asn [N]	2	1074

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs2228220 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838973.1	8399928	12054891	plus	A	alt_assembly_8	HuRef	HuRef	view	300
6	NT_007592.14	2981507	12231235	plus	A	ref_assembly	reference	reference	view	300
6	NW_922984.1	11746560	13351304	plus	A	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007615.6

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank mRNA:
NM_002114.2	AL391828.10	M32019.1 X51435.1

UniGene Cluster ID
549037

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A	A/A	A/G	G	G/G	N	HWP	A	G	N
ss23756835	AFD_EUR_PANEL	European	48	IG		0.833	0.167				0.752	0.917	0.083

	AFD_AFR_PANEL	African American	46	IG		0.696	0.217		0.087		0.150	0.804	0.196

	AFD_CHN_PANEL	Asian	48	IG		0.833	0.125		0.042		0.150	0.896	0.104

ss3172881	WIAF-CSNP-MITOGPOP5	multiple	62	IG		0.806	0.194				0.584	0.903	0.097

	CHMJ	Asian	74	IG	0.946			0.041		0.014		0.946	0.041	0.014

ss48428064	HapMap-CEU	European	120	IG		0.767	0.233				0.317	0.883	0.117

	HapMap-HCB	Asian	90	IG		0.800	0.200				0.479	0.900	0.100

	HapMap-JPT	Asian	88	IG		0.795	0.205				0.479	0.898	0.102

	HapMap-YRI	Sub-Saharan African	120	IG		0.600	0.350		0.050		1.000	0.775	0.225

	AGI_ASP population	multiple	72	IG		0.861	0.139				0.655	0.931	0.069

ss66136525	HapMap-CEU	European	118	GF		0.763	0.237					0.881	0.119

	HapMap-HCB	Asian	90	GF		0.800	0.200					0.900	0.100

	HapMap-JPT	Asian	90	GF		0.800	0.200					0.900	0.100

	HapMap-YRI	Sub-Saharan African	120	GF		0.600	0.367		0.033			0.783	0.217

ss68965490	HapMap-CEU	European	120	GF		0.767	0.233					0.883	0.117

	HapMap-HCB	Asian	90	GF		0.800	0.200					0.900	0.100

	HapMap-JPT	Asian	90	GF		0.800	0.200					0.900	0.100

	HapMap-YRI	Sub-Saharan African	120	GF		0.600	0.350		0.050			0.775	0.225

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss23756835	71	56	12	3
ss3172881	31	25	6
ss48428064	308	225	76	3
ss66136525	268
ss68965490	269	195	71	3

RefSNP Genotype Summary	Total Individual	A	A/A	A/G	G	G/G	N
rs2228220	395		295	91		6

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5134	ss48428064	G/G	CSHL-HAPMAP	HapMap-YRI	NA19127	YOR077.02	r23_ch6_YRI_illumina:golden_gate_1.0.0	551316
5134	ss66136525	C/T	CSHL-HAPMAP	HapMap-YRI	NA19127	YOR077.02	chr6-HapMap-YRI
5134	ss68965490	G/G	CSHL-HAPMAP	HapMap-YRI	NA19127	YOR077.02	chr6-HapMap-YRI

Genotype data submitted for	411	samples from	395	individuals	Individual with multiple genotypes submission:	274

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: PERLEGEN

UNKNOWN

YES

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Revised: May 25, 2006 1:38 PM .