Reference SNP(refSNP) Cluster Report: rs3744786

Reference SNP(refSNP) Cluster Report: rs3744786

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	107/130
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_002278.3:c.215A>G
NP_002269.3:p.Gln72Arg
NT_010755.15:g.3347659T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss90587799 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3744786 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
ss4930794	YUSUKE\|IMS-JST096180	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	08/01/02	10/10/03	107	Genomic	unknown
ss24098689	PERLEGEN\|afd4241907	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	08/10/04	09/13/04	123	Genomic	unknown
ss65727655	ILLUMINA\|Human1-rs3744786	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	10/10/06	10/10/06	127	Genomic	unknown
ss66681310	ILLUMINA\|HumanHap300v1.1_rs3744786	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	11/09/06	11/09/06	127	Genomic	unknown
ss67298873	ILLUMINA\|HumanHap550v1.1_rs3744786	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	11/14/06	11/14/06	127	Genomic	unknown
ss67703487	ILLUMINA\|HumanHap650Yv1.0_rs3744786	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	11/14/06	11/14/06	127	Genomic	unknown
ss69196312	PERLEGEN\|PGP04241907	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	01/30/07	03/31/08	127	Genomic	unknown
ss70777504	ILLUMINA\|HumanHap550v3.0__rs3744786	rev/T	A/G	tctccaaaacctatctatccagttcctgcc	ggcagccagtggcatctccggctccatggg	04/20/07	03/30/08	130	Genomic	unknown
ss71353657	ILLUMINA\|HumanHap650Yv3.0_rs3744786	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	04/23/07	04/23/07	127	Genomic	unknown
ss75567999	ILLUMINA\|ILMN_Human_1M_rs3744786	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	08/28/07	08/29/07	129	Genomic	unknown
ss78041770	HGSV\|Cor12878_SNV_20070510.chr17_36876889	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	10/17/07	10/17/07	129	Genomic	unknown
ss79164261	ILLUMINA\|HumanHap300v2.0_rs3744786	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	04/18/07	11/18/07	130	Genomic	unknown
ss81095933	HGSV\|Cor18555_SNV_20070510.chr17_36876889	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	11/27/07	11/27/07	130	Genomic	unknown
ss84165423	KRIBB_YJKIM\|KHS648743	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	12/04/07	12/06/07	130	Genomic	unknown
ss90587799	BCMHGSC_JDW\|JWB-1021260	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	02/26/08	02/29/08	129	Genomic	unknown
ss109763210	1000GENOMES\|CEU.trio.12.15.2008_3398551_chr17_36876889	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	12/15/08	12/16/08	130	Genomic	unknown
ss118054012	ILLUMINA-UK\|NA18507_000043071_NCBI36.1_chr17_36876889	fwd/B	C/T	cccatggagccggagatgccactggctgcc	ggcaggaactggatagataggttttggaga	01/20/09	01/20/09	130	Genomic	99 %

Fasta sequence (Legend)

 CTGCTGGAGC TCCTCAATGG TCCTGAAATG AGACTGGTAG TCAGGAGTCA TGGTGAGCAC
 CTGGGAGTGA GAGGCCTCTT GGATCCTGCT CTCCAGCTCC GCATTCTCCT GCTCCAGCTG
 CCGCACCCTC GTCAGGTAGC TGGCCAGGCG GTCGTTAAGG AACTGCATGG TTTCCTTCTC
 ATTGCCATTG AAGGCCCCTT CGCTGTACCA GCTGCCGGGG CCCATGGAGC CGGAGATGCC
 ACTGGCTGCC
 Y
 GGCAGGAACT GGATAGATAG GTTTTGGAGA GGCAGCTGGC TGGCCGGAAG GTGGTGGGCA
 GGCAGACCGA AGGCAGGCAT GCCATGGGCT GGCAGACATA GCCCAGGCAC AGCTCAGGCC
 GGCAGTTCAC GCCGCTGGAA CAGACCGAGG CAGGCCGGGG GCAGCTCTTG AGAGAGGCTT
 GCAAGTTGTT GGTGACACAG CAGGAGGATG TCATGTTGGA GAGGCCCTTT CTCCTCAGCC
 ACAGCTACCT

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_010842.1

dbSNP Blast Analysis

UniGene Cluster ID
41752

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss24098689	AFD_EUR_PANEL	European	48	IG	0.042	0.500	0.458	0.317	0.292		0.708

	AFD_AFR_PANEL	African American	46	IG		0.261	0.739	0.479	0.130		0.870

	AFD_CHN_PANEL	Asian	46	IG	0.043	0.522	0.435	0.273	0.304		0.696

	HapMap-CEU	European	120	IG	0.100	0.433	0.467	1.000	0.317		0.683

	HapMap-HCB	Asian	90	IG	0.133	0.422	0.444	0.752	0.344		0.656

	HapMap-JPT	Asian	90	IG	0.111	0.444	0.444	1.000	0.333		0.667

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.250	0.733	1.000	0.142		0.858

	CHMJ	Asian	74	IG					0.257	0.014	0.730

ss4930794	JBIC-allele		1498	AF					0.290		0.710

ss69196312	HapMap-CEU	European	120	GF	0.067	0.500	0.433		0.317		0.683

	HapMap-HCB	Asian	90	GF	0.067	0.511	0.422		0.322		0.678

	HapMap-JPT	Asian	90	GF	0.044	0.533	0.422		0.311		0.689

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.250	0.733		0.142		0.858

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24098689	71	2	30	38
ss90587799	1187	92	502	568

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs3744786	1263	94	526	601

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
185	ss90587799	C/C	CSHL-HAPMAP	HapMap-CEU	NA07055	CEPH1341.12	r27_ch17_CEU_illumina:human_1m_beadchip
187	ss90587799	C/T	CSHL-HAPMAP	HapMap-CEU	NA06985	CEPH1341.14	r27_ch17_CEU_illumina:human_1m_beadchip
225	ss90587799	C/C	CSHL-HAPMAP	HapMap-CEU	NA12043	CEPH1346.11	r27_ch17_CEU_illumina:human_1m_beadchip
226	ss90587799	T/T	CSHL-HAPMAP	HapMap-CEU	NA12044	CEPH1346.12	r27_ch17_CEU_illumina:human_1m_beadchip
361	ss90587799	T/T	CSHL-HAPMAP	HapMap-CEU	NA11993	CEPH1362.14	r27_ch17_CEU_illumina:human_1m_beadchip
620	ss90587799	T/T	CSHL-HAPMAP	HapMap-CEU	NA12874	CEPH1459.11	r27_ch17_CEU_illumina:human_1m_beadchip
5151	ss90587799	C/C	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	r27_ch17_CHB_illumina:human_1m_beadchip
5165	ss90587799	C/C	CSHL-HAPMAP	HapMap-HCB	NA18608	CH18608	r27_ch17_CHB_illumina:human_1m_beadchip
5174	ss90587799	T/T	CSHL-HAPMAP	HapMap-HCB	NA18571	CH18571	r27_ch17_CHB_illumina:human_1m_beadchip
5175	ss90587799	C/C	CSHL-HAPMAP	HapMap-HCB	NA18620	CH18620	r27_ch17_CHB_illumina:human_1m_beadchip
5201	ss90587799	T/T	CSHL-HAPMAP	HapMap-JPT	NA18948	JA18948	r27_ch17_JPT_illumina:human_1m_beadchip
5207	ss90587799	C/C	CSHL-HAPMAP	HapMap-JPT	NA18959	JA18959	r27_ch17_JPT_illumina:human_1m_beadchip
5208	ss90587799	C/T	CSHL-HAPMAP	HapMap-JPT	NA18969	JA18969	r27_ch17_JPT_illumina:human_1m_beadchip
5212	ss90587799	T/T	CSHL-HAPMAP	HapMap-JPT	NA18965	JA18965	r27_ch17_JPT_illumina:human_1m_beadchip
5215	ss90587799	C/C	CSHL-HAPMAP	HapMap-JPT	NA18975	JA18975	r27_ch17_JPT_illumina:human_1m_beadchip
5225	ss90587799	C/C	CSHL-HAPMAP	HapMap-JPT	NA18987	JA18987	r27_ch17_JPT_illumina:human_1m_beadchip
5241	ss90587799	T/T	CSHL-HAPMAP	HapMap-YRI	NA18506	YOR009.01	r27_ch17_YRI_illumina:human_1m_beadchip
5249	ss90587799	C/T	CSHL-HAPMAP	HapMap-YRI	NA18516	YOR013.03	r27_ch17_YRI_illumina:human_1m_beadchip
5255	ss90587799	T/T	CSHL-HAPMAP	HapMap-YRI	NA18871	YOR017.03	r27_ch17_YRI_illumina:human_1m_beadchip
5265	ss90587799	C/T	CSHL-HAPMAP	HapMap-YRI	NA18914	YOR028.01	r27_ch17_YRI_illumina:human_1m_beadchip

Genotype data submitted for	1278	samples from	1263	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 .