Reference SNP(refSNP) Cluster Report: rs2236387

Reference SNP(refSNP) Cluster Report: rs2236387

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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_017825.1:c.625G>A
NP_060295.1:p.Glu209Lys
NT_032977.8:g.6529537G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44123189 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2236387 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
ss3190757	YUSUKE\|IMS-JST016668	fwd/B	C/T	tgtggcccaggagttgcttgagaaagtgct	gctggaagactcgccctgcaaggccaggtg	08/07/01	10/10/03	98	Genomic	unknown
ss16225075	CGAP-GAI\|1457726	rev/T	A/G	cacctggccttgcagggcgagtcttccagc	agcactttctcaagcaactcctgggccaca	11/18/03	11/22/03	120	cDNA	unknown
ss19863597	CSHL-HAPMAP\|CSHL-HuFF-200402.chr1.NT_079482.1_1259365	rev/T	A/G	cacctggccttgcagggcgagtcttccagc	agcactttctcaagcaactcctgggccaca	02/21/04	03/04/04	120	Genomic	unknown
ss24150939	PERLEGEN\|afd4530145	rev/T	A/G	cacctggccttgcagggcgagtcttccagc	agcactttctcaagcaactcctgggccaca	08/10/04	09/13/04	123	Genomic	unknown
ss44123189	ABI\|hCV11858717	rev/T	A/G	cacctggccttgcagggcgagtcttccagc	agcactttctcaagcaactcctgggccaca	07/18/05	11/03/06	126	Genomic	unknown
ss48429184	APPLERA_GI\|hCV11858717	fwd/B	C/T	tgtggcccaggagttgcttgagaaagtgct	gctggaagactcgccctgcaaggccaggtg	09/28/05	11/03/06	126	Genomic	unknown
ss65731021	ILLUMINA\|Human1-rs2236387	fwd/B	C/T	tgtggcccaggagttgcttgagaaagtgct	gctggaagactcgccctgcaaggccaggtg	10/10/06	10/10/06	127	Genomic	unknown
ss68763432	PERLEGEN\|PGP04530145	rev/T	A/G	cacctggccttgcagggcgagtcttccagc	agcactttctcaagcaactcctgggccaca	01/30/07	08/14/07	127	Genomic	unknown
ss74807626	AFFY\|SNP_M-178518	fwd/B	C/T	tgtggcccaggagttgcttgagaaagtgct	gctggaagactcgccctgcaaggccaggtg	08/09/07	08/09/07	128	Genomic	unknown
ss74878784	ILLUMINA\|ILMN_Human_1M_rs2236387	fwd/B	C/T	tgtggcccaggagttgcttgagaaagtgct	gctggaagactcgccctgcaaggccaggtg	08/28/07	08/29/07	129	Genomic	unknown
ss76441305	AFFY\|AFFY_6_1M_SNP_A-8302085	rev/T	A/G	gggcgagtcttccagc	agcactttctcaagca	08/28/07	08/30/07	130	Genomic	unknown
ss86178346	HGSV\|Cor18956_SNV_20070510.chr1_36226712	rev/T	A/G	cacctggccttgcagggcgagtcttccagc	agcactttctcaagcaactcctgggccaca	11/30/07	12/11/07	130	Genomic	unknown
ss104866946	KRIBB_YJKIM\|KHS1259264	fwd/B	C/T	tgtggcccaggagttgcttgagaaagtgct	gctggaagactcgccctgcaaggccaggtg	07/10/08	07/10/08	130	Genomic	unknown

Fasta sequence (Legend)

 GCAGCCAGGC ACAGGTGCCG ACAAGAGGTG GGAGAGGGCT GGGGTGAGCA GGTCGTTTCG
 TTCTCTGGGA CCCTGAGAGC CTTGAAACAT AGACAAGATA AAGGGGCTTC TGCCCATGCC
 TCCCTAGGGT CTGCAATTGA GGAAGGTTTA CAGTTTGCGG CAATGCCAGA GGCCCCCTGG
 ATCACCCACA TACCCACACC ACACACCTCC AGCCCCATAC TCACTCCCTG GCATCCAAGA
 CGGACTGGGC ATCACCCTCC AGATCCTCCA TGTGGCCCAG GAGTTGCTTG AGAAAGTGCT
 Y
 GCTGGAAGAC TCGCCCTGCA AGGCCAGGTG CACAGCCAGG GCCTGCAGGA TGGCGCCATT
 GTAACCCAGG GAGGAGGCGT GTGTCAGCTG GGCCGAGAGC CGGGCAAACT AGGGAGGAGG
 AGACCTGCTG TCACAGAAGC CCTGCTGCAG AAGAGGAAGG GGACAGCCCA GAAGCCAGCC
 CGCCCTGAAT ACCTTCTGCA CATCCTGGAC ACTGCTATAG GCCAGGGAGA TGCCAGCCAC
 CCGCATGGCA CCTCCATTGC CATAGGAGCC TTTCCCGTTA AACTGGGCCC GGGCAGGCTC

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_079482 BI768017

dbSNP Blast Analysis

UniGene Cluster ID
18021

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss24150939	AFD_EUR_PANEL	European	48	IG	1.000				1.000

	AFD_AFR_PANEL	African American	40	IG	0.600	0.400		0.273	0.800	0.200

	AFD_CHN_PANEL	Asian	44	IG	0.591	0.273	0.136	0.150	0.727	0.273

ss3190757	JBIC-allele		1488	AF					0.652	0.348

ss44123189	HapMap-CEU	European	120	IG	0.983	0.017		1.000	0.992	0.008

	HapMap-HCB	Asian	90	IG	0.444	0.511	0.044	0.150	0.700	0.300

	HapMap-JPT	Asian	88	IG	0.455	0.386	0.159	0.317	0.648	0.352

	HapMap-YRI	Sub-Saharan African	120	IG	0.467	0.400	0.133	0.439	0.667	0.333

	AoD_African_American		90	AF					0.820	0.180

	AoD_Chinese		90	AF					0.810	0.190

	AoD_Japanese		90	AF					0.550	0.450

ss48429184	AGI_ASP population	multiple	60	IG	0.833	0.167		0.655	0.917	0.083

ss68763432	HapMap-CEU	European	120	GF	0.967	0.017	0.017		0.975	0.025

	HapMap-HCB	Asian	90	GF	0.467	0.378	0.156		0.656	0.344

	HapMap-JPT	Asian	90	GF	0.467	0.356	0.178		0.644	0.356

	HapMap-YRI	Sub-Saharan African	120	GF	0.467	0.300	0.233		0.617	0.383

Concordant Genotype	Total Sample	C/C	C/T
ss24150939	71
ss44123189	1191
ss48429184	32	25	5

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs2236387	1295	25	5

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
226	ss44123189	G/G	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r27_ch1_CEU_illumina:human_1m_beadchip	208468
5135	ss44123189	A/G	CSHL-HAPMAP	HapMap-YRI	NA19128	YOR077.03	r27_ch1_YRI_illumina:human_1m_beadchip	208468
5149	ss44123189	A/G	CSHL-HAPMAP	HapMap-HCB	NA18524	CH18524	r27_ch1_CHB_illumina:human_1m_beadchip	208468
5150	ss44123189	A/G	CSHL-HAPMAP	HapMap-HCB	NA18529	CH18529	r27_ch1_CHB_illumina:human_1m_beadchip	208468
5157	ss44123189	N/N	CSHL-HAPMAP	HapMap-HCB	NA18540	CH18540	r27_ch1_CHB_illumina:human_1m_beadchip	208468
5175	ss44123189	A/G	CSHL-HAPMAP	HapMap-HCB	NA18620	CH18620	r27_ch1_CHB_illumina:human_1m_beadchip	208468
5188	ss44123189	A/G	CSHL-HAPMAP	HapMap-HCB	NA18635	CH18635	r27_ch1_CHB_illumina:human_1m_beadchip	208468
5190	ss44123189	A/G	CSHL-HAPMAP	HapMap-HCB	NA18636	CH18636	r27_ch1_CHB_illumina:human_1m_beadchip	208468
5213	ss44123189	A/G	CSHL-HAPMAP	HapMap-JPT	NA18973	JA18973	r27_ch1_JPT_illumina:human_1m_beadchip	208468
5256	ss44123189	A/G	CSHL-HAPMAP	HapMap-YRI	NA18854	YOR018.01	r27_ch1_YRI_illumina:human_1m_beadchip	208468
5263	ss44123189	A/G	CSHL-HAPMAP	HapMap-YRI	NA18861	YOR024.02	r27_ch1_YRI_illumina:human_1m_beadchip	208468
5267	ss44123189	A/G	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	r27_ch1_YRI_illumina:human_1m_beadchip	208468
5276	ss44123189	A/G	CSHL-HAPMAP	HapMap-YRI	NA19138	YOR043.03	r27_ch1_YRI_illumina:human_1m_beadchip	208468
5290	ss44123189	A/G	CSHL-HAPMAP	HapMap-YRI	NA19206	YOR051.02	r27_ch1_YRI_illumina:human_1m_beadchip	208468
5307	ss44123189	N/N	CSHL-HAPMAP	HapMap-YRI	NA19145	YOR074.01	r27_ch1_YRI_illumina:human_1m_beadchip	208468
5308	ss44123189	A/G	CSHL-HAPMAP	HapMap-YRI	NA19143	YOR074.02	r27_ch1_YRI_illumina:human_1m_beadchip	208468

Genotype data submitted for	1310	samples from	1295	individuals	Individual with multiple genotypes submission:	15

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 .