Reference SNP(refSNP) Cluster Report: rs1138357

Reference SNP(refSNP) Cluster Report: rs1138357

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/130
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_001114735.1:c.56G>A
NM_004049.2:c.56G>A
NM_004049.3:c.56G>A
NP_001108207.1:p.Cys19Tyr
NP_004040.1:p.Cys19Tyr
NT_010194.16:g.51053726C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48418002 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1138357 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
ss1545748	LEE\|897919	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	09/13/00	10/10/03	86	cDNA	unknown
ss2982426	AFFX\|AFFX_SNP-1171	fwd/T	A/G	aggctggctcaggactatctgcagt	cgtcctacagataccacaacctgga	05/21/01	10/10/03	100	Genomic	unknown
ss4431280	LEE\|e897919	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	04/26/02	10/10/03	106	cDNA	unknown
ss4929432	YUSUKE\|IMS-JST094676	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	07/29/02	05/16/04	108	Genomic	unknown
ss24064952	PERLEGEN\|afd4527483	rev/B	C/T	cctgatccaggttgtggtatctgtaggacg	actgcagatagtcctgagccagcctgtaaa	08/10/04	09/13/04	126	Genomic	unknown
ss48418002	APPLERA_GI\|hCV7509650	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	09/28/05	11/03/06	126	Genomic	unknown
ss65725335	ILLUMINA\|Human1-rs1138357	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	10/10/06	10/10/06	127	Genomic	unknown
ss66550946	ILLUMINA\|HumanHap300v1.1_rs1138357	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	11/09/06	11/09/06	127	Genomic	unknown
ss66930304	ILLUMINA\|HumanHap550v1.1_rs1138357	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	11/14/06	11/14/06	127	Genomic	unknown
ss67088084	ILLUMINA\|HumanHap650Yv1.0_rs1138357	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	11/14/06	11/14/06	127	Genomic	unknown
ss69182212	PERLEGEN\|PGP04527483	rev/B	C/T	cctgatccaggttgtggtatctgtaggacg	actgcagatagtcctgagccagcctgtaaa	01/30/07	08/14/07	127	Genomic	unknown
ss70393587	ILLUMINA\|HumanHap300v2.0_rs1138357	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	04/18/07	11/18/07	127	Genomic	unknown
ss70528287	ILLUMINA\|HumanHap550v3.0__rs1138357	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	04/20/07	03/30/08	130	Genomic	unknown
ss71058565	ILLUMINA\|HumanHap650Yv3.0_rs1138357	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	04/23/07	04/23/07	127	Genomic	unknown
ss74809008	AFFY\|SNP_M-181349	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	08/09/07	08/09/07	128	Genomic	unknown
ss75744620	ILLUMINA\|ILMN_Human_1M_rs1138357	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	08/28/07	08/29/07	129	Genomic	unknown
ss83398476	HGSV\|Cor18956_SNV_20070510.chr15_78050461	rev/B	C/T	cctgatccaggttgtggtatctgtaggacg	actgcagatagtcctgagccagcctgtaaa	11/30/07	12/04/07	130	Genomic	unknown
ss83687532	KRIBB_YJKIM\|KHS519568	fwd/T	A/G	tttacaggctggctcaggactatctgcagt	cgtcctacagataccacaacctggatcagg	12/04/07	12/05/07	130	Genomic	unknown
ss86348151	CANCER-GENOME\|1555	rev/B	C/T	cctgatccaggttgtggtatctgtaggacg	actgcagatagtcctgagccagcctgtaaa	01/25/08	01/25/08	129	Genomic	unknown
ss90225505	BCMHGSC_JDW\|JWB-0883471	rev/B	C/T	cctgatccaggttgtggtatctgtaggacg	actgcagatagtcctgagccagcctgtaaa	02/26/08	02/29/08	129	Genomic	unknown
ss106443786	BGI\|BGI_rs1138357	rev/B	C/T	cctgatccaggttgtggtatctgtaggacg	actgcagatagtcctgagccagcctgtaaa	09/15/08	06/18/09	130	Genomic	unknown
ss108976002	1000GENOMES\|CEU.trio.12.15.2008_3203089_chr15_78050461	rev/B	C/T	cctgatccaggttgtggtatctgtaggacg	actgcagatagtcctgagccagcctgtaaa	12/15/08	12/16/08	130	Genomic	unknown
ss114436896	1000GENOMES\|NA19240_2008_12_16_2872380_chr15_78050461	rev/B	C/T	cctgatccaggttgtggtatctgtaggacg	actgcagatagtcctgagccagcctgtaaa	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 TTCTCTGAAA CATTTTCCTC TTTCACATTT TAAACTTTCT CTTTCATACA TGACATGAAA
 CACAGCCTAC GCACGAAAGT GACTAGGAGG AAGGATATTA TAAAGTGATG CAAACAGAAA
 TTCCACCAGC CTCCATGTAT CATCATGTGT CATAACTCAG TCAAGCTCAG TGAGCATTCT
 CAGCACATTG CCTCAACAGC TTCAAGGTGA GCCAGCTCAA GACTTTGCTC TCCACCAGGC
 AGAAGATGAC AGACTGTGAA TTTGGATATA TTTACAGGCT GGCTCAGGAC TATCTGCAGT
 R
 CGTCCTACAG ATACCACAAC CTGGATCAGG TCCAAGCAAA ACGTCCAGAG TGCTACAAAA
 TGTTGCGTTC TCAGTCCAAA AAGAAGTGGA AAAGAATCTG AAGTCATGCT TGGACAATGT
 TAATGTTGTG TCCGTAGACA CTGCCAGAAC ACTATTCAAC CAAGTGATGG AAAAGGAGTT
 TGAAGACGGC ATCATTAACT GGGGAAGAAT TGTAACCATA TTTGCATTTG AAGGTATTCT
 CATCAAGAAA CTTCTACGAC AGCAAATTGC CCCGGATGTG GATACCTATA AGGAGATTTC

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
U29680 Hs.227817

dbSNP Blast Analysis

UniGene Cluster ID
227817

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss24064952	AFD_EUR_PANEL	European	48	IG		0.292	0.708	0.439	0.146	0.854

	AFD_AFR_PANEL	African American	46	IG	0.043	0.304	0.652	1.000	0.196	0.804

	AFD_CHN_PANEL	Asian	48	IG	0.208	0.583	0.208	0.439	0.500	0.500

	CHMJ	Asian	74	IG					0.500	0.500

ss48418002	HapMap-CEU	European	120	IG	0.033	0.433	0.533	0.251	0.250	0.750

	HapMap-HCB	Asian	90	IG	0.289	0.422	0.289	0.317	0.500	0.500

	HapMap-JPT	Asian	88	IG	0.318	0.432	0.250	0.403	0.534	0.466

	HapMap-YRI	Sub-Saharan African	120	IG	0.033	0.367	0.600	0.584	0.217	0.783

	AGI_ASP population	multiple	78	IG	0.026	0.462	0.513	0.200	0.256	0.744

ss4929432	CEPH		184	AF					0.480	0.520

ss69182212	HapMap-CEU	European	120	GF	0.033	0.433	0.533		0.250	0.750

	HapMap-HCB	Asian	90	GF	0.289	0.422	0.289		0.500	0.500

	HapMap-JPT	Asian	88	GF	0.295	0.432	0.273		0.511	0.489

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

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss24064952	71
ss48418002	1245	160	516	534
ss69182212	269

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs1138357	1302	160	516	534

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
175	ss48418002	G/G	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	r27_ch15_CEU_illumina:human_1m_beadchip
175	ss69182212	C/T	CSHL-HAPMAP	HapMap-CEU	NA06991	CEPH1341.02	chr15-HapMap-CEU

Genotype data submitted for	1317	samples from	1302	individuals	Individual with multiple genotypes submission:	276

Validation Summary:

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

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Revised: May 25, 2006 1:38 PM .