Reference SNP(refSNP) Cluster Report: rs1154510

Reference SNP(refSNP) Cluster Report: rs1154510

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/130
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_002150.2:c.97G>A
NP_002141.1:p.Ala33Thr
NT_009775.16:g.12864844T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1593356 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1154510 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
ss1593356	KWOK\|OVLP-000925-281423	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	10/04/00	05/16/04	87	Genomic	99 %
ss1593669	KWOK\|OVLP-000925-284745	fwd/T	A/G	gaaccctgctgcaaccctgtgattcaggcc	cgtcattctactgcagcaagatgggctttg	10/04/00	10/10/03	87	Genomic	99 %
ss2662905	SC_JCM\|AC079360.4_26602	fwd/T	A/G	gaaccctgctgcaaccctgtgattcaggcc	cgtcattctactgcagcaagatgggctttg	11/03/00	10/10/03	89	Genomic	unknown
ss4927589	YUSUKE\|IMS-JST092614	fwd/T	A/G	gaaccctgctgcaaccctgtgattcaggcc	cgtcattctactgcagcaagatgggctttg	07/29/02	10/10/03	108	Genomic	unknown
ss11037815	BCM_SSAHASNP\|chr12.NT_009487.15_263206	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	07/01/03	10/10/03	116	Genomic	unknown
ss16292253	SC_SNP\|NT_009487.15_263206	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	11/18/03	11/22/03	120	Genomic	unknown
ss20903900	SSAHASNP\|WGSA-200403-chr12.chr12.NT_009487.15_263206	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	03/19/04	03/19/04	121	Genomic	unknown
ss23934720	PERLEGEN\|afd4139353	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	08/10/04	09/13/04	123	Genomic	unknown
ss28511022	MGC_GENOME_DIFF\|BC024287x29804225-T263206C	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	08/25/04	08/25/04	126	cDNA	unknown
ss69123212	PERLEGEN\|PGP04139353	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	01/30/07	08/14/07	127	Genomic	unknown
ss74812461	AFFY\|SNP_M-287588	fwd/T	A/G	gaaccctgctgcaaccctgtgattcaggcc	cgtcattctactgcagcaagatgggctttg	08/09/07	08/09/07	128	Genomic	unknown
ss74889496	ILLUMINA\|ILMN_Human_1M_rs1154510	fwd/T	A/G	gaaccctgctgcaaccctgtgattcaggcc	cgtcattctactgcagcaagatgggctttg	08/28/07	08/29/07	129	Genomic	unknown
ss84892433	HGSV\|Cor19240_SNV_20070510.chr12_120758055	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	11/30/07	12/08/07	130	Genomic	unknown
ss97258048	HUMANGENOME_JCVI\|1103649556534	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	03/28/08	03/28/08	130	Genomic	unknown
ss112493464	1000GENOMES\|CEU.trio.12.15.2008_2824978_chr12_120779718	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	12/15/08	12/17/08	130	Genomic	unknown
ss114204662	1000GENOMES\|NA19240_2008_12_16_2542707_chr12_120779718	rev/B	C/T	caaagcccatcttgctgcagtagaatgacg	ggcctgaatcacagggttgcagcagggttc	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 TACTCTGAAT CCTAATTACA CCAGCGGGAA AGTTATCTGT CAGCAAAATG TGCAGGCAGC
 AGTCTATCTT CCCAGGAGGG TCTCTGCCCC TGAGGCAATA GGGCAGGCAG GCTGAGGGGG
 GCCAGGGGCT CTCTTGCGGA AGTCCCCCAT GCTGGCCCCT TGACCCTCAT GAACCCTGCT
 GCAACCCTGT GATTCAGGCC
 R
 CGTCATTCTA CTGCAGCAAG ATGGGCTTTG AACCTCTAGC CTACAGGGGC CTGGAGACCG
 GTTCCCGGGA GGTGGTCAGC CATGTAATCA AACAAGGGAA GGTGAGTCAC CACCCCCAGG
 ACAGCCCCCA ACCcctgcct ggccaacatg gtgaaacccc atctctatta aaaatagaaa
 aattagctgg gcatgatggt gggcacctgt aatcccagct actcaggagg ctgaggcagg
 cacatcgctt gaacccggga ggcagaggtt gcagtgagcc aacgtcgtgc cactgcactc
 cagcctgggc gacagagcaa gactccatct caacaaaaaa aaacaaaaaa caacaaaaaa
 CCCCAACAAC AACAACAAAA ACATATAATT CAGCTCCCAC CGACCCCTCC GCTGGCATCT
 TTGTACAGCC ATGCAACACG GCCCTTCCTA GTTTCGTTTC

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_009487.1 ABBA01020186 AC022460 AC079360.4 BC024287

dbSNP Blast Analysis

UniGene Cluster ID
2899

Population Diversity

	Sample Ascertainment				Genotype Detail							Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	C/C	C/T	G/G	T/T	HWP	A	C	G	T
ss1593356	CEPH		184	AF								0.190		0.810

	HapMap-CEU	European	120	IG	0.017	0.200			0.783		1.000	0.117		0.883

	HapMap-HCB	Asian	90	IG		0.244			0.756		0.371	0.122		0.878

	HapMap-JPT	Asian	90	IG	0.044	0.311			0.644		1.000	0.200		0.800

	HapMap-YRI	Sub-Saharan African	120	IG		0.083			0.917		0.752	0.042		0.958

	EURAME		32	GF				0.312		0.688			0.156		0.844

	AFRAME		30	GF				0.133		0.867			0.067		0.933

ss23934720	AFD_EUR_PANEL	European	48	IG		0.208			0.792		0.584	0.104		0.896

	AFD_AFR_PANEL	African American	46	IG		0.087			0.913		1.000	0.043		0.957

	AFD_CHN_PANEL	Asian	46	IG	0.043	0.435			0.522		0.584	0.261		0.739

ss69123212	HapMap-CEU	European	120	GF	0.017	0.183			0.800			0.108		0.892

	HapMap-HCB	Asian	90	GF		0.244			0.756			0.122		0.878

	HapMap-JPT	Asian	90	GF	0.044	0.311			0.644			0.200		0.800

	HapMap-YRI	Sub-Saharan African	120	GF		0.083			0.917			0.042		0.958

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss1593356	1206	928	236	18
ss23934720	71	52	17	1
ss69123212	269	215	50	4
ss97258048	1	1

RefSNP Genotype Summary	Total Individual	A/A	A/G	C/C	C/T	G/G	T/T
rs1154510	1264			992	251		19

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
172	ss1593356	C/C	CSHL-HAPMAP	HapMap-CEU	NA07056	CEPH1340.12	r27_ch12_CEU_illumina:human_1m_beadchip	4573473
172	ss69123212	C/C	CSHL-HAPMAP	HapMap-CEU	NA07056	CEPH1340.12	chr12-HapMap-CEU

Genotype data submitted for	1279	samples from	1264	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

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .