Reference SNP(refSNP) Cluster Report: rs1128400

Reference SNP(refSNP) Cluster Report: rs1128400

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

HGVS Names
NM_001024732.1:c.58T>C
NM_016011.2:c.286T>C
NP_001019903.1:p.Phe20Leu
NP_057095.2:p.Phe96Leu
NT_004610.18:g.12366979A>G

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss76890942 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1128400 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
ss1515627	LEE\|171728	fwd/B	C/T	gacataaatatgatccaaggaaactacgga	tccttcctgaactgcctgctgttggaggga	09/13/00	10/10/03	86	cDNA	unknown
ss4228434	SC_JCM\|AL590729.4_88298	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	10/15/01	10/10/03	102	Genomic	unknown
ss4408418	LEE\|e171728	fwd/B	C/T	gacataaatatgatccaaggaaactacgga	tccttcctgaactgcctgctgttggaggga	04/26/02	10/10/03	110	cDNA	unknown
ss4924063	YUSUKE\|IMS-JST083773	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	07/24/02	10/10/03	108	Genomic	unknown
ss9808055	BCM_SSAHASNP\|chr1.NT_004538.14_735593	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	06/27/03	10/10/03	116	Genomic	unknown
ss16240684	CGAP-GAI\|1478513	fwd/B	C/T	gacataaatatgatccaaggaaactacgga	tccttcctgaactgcctgctgttggaggga	11/18/03	11/22/03	126	cDNA	unknown
ss19124444	CSHL-HAPMAP\|CSHL-HuDD-200402.chr1.NT_004538.15_731943	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	02/20/04	05/16/04	120	Genomic	unknown
ss24150391	PERLEGEN\|afd1002487	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	08/10/04	09/13/04	123	Genomic	unknown
ss28510351	MGC_GENOME_DIFF\|BC001419x37548196-A731943G	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	08/25/04	08/25/04	126	cDNA	unknown
ss41288357	ABI\|hCV452600	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	07/16/05	11/03/06	126	Genomic	unknown
ss48422184	APPLERA_GI\|hCV452600	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	09/28/05	11/03/06	126	Genomic	unknown
ss65725291	ILLUMINA\|Human1-rs1128400	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	10/10/06	10/10/06	127	Genomic	unknown
ss66668165	ILLUMINA\|HumanHap300v1.1_rs1128400	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	11/09/06	11/09/06	127	Genomic	unknown
ss66930138	ILLUMINA\|HumanHap550v1.1_rs1128400	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	11/14/06	11/14/06	127	Genomic	unknown
ss67087730	ILLUMINA\|HumanHap650Yv1.0_rs1128400	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	11/14/06	11/14/06	127	Genomic	unknown
ss68762156	PERLEGEN\|PGP01002487	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	01/30/07	08/14/07	127	Genomic	unknown
ss70393449	ILLUMINA\|HumanHap300v2.0_rs1128400	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	04/18/07	11/18/07	127	Genomic	unknown
ss70528123	ILLUMINA\|HumanHap550v3.0__rs1128400	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	04/20/07	03/30/08	130	Genomic	unknown
ss71058390	ILLUMINA\|HumanHap650Yv3.0_rs1128400	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	04/23/07	04/23/07	127	Genomic	unknown
ss74807637	AFFY\|SNP_M-178510	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	08/09/07	08/09/07	128	Genomic	unknown
ss75586956	ILLUMINA\|ILMN_Human_1M_rs1128400	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	08/28/07	08/29/07	129	Genomic	unknown
ss76890942	SI_EXO\|NT_004610.18_12366979	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	09/20/07	09/20/07	129	Genomic	unknown
ss80646385	HGSV\|Cor18507_SNV_20070510.chr1_29363253	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	11/23/07	11/26/07	130	Genomic	unknown
ss83686689	KRIBB_YJKIM\|KHS519369	fwd/B	C/T	taatgctcttctccctcaggaaactacgga	tccttcctgaactgcctgctgttggaggga	12/04/07	12/05/07	130	Genomic	unknown
ss85939218	HGSV\|Cor19129_SNV_20070510.chr1_29363253	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	12/06/07	12/10/07	130	Genomic	unknown
ss87324618	BCMHGSC_JDW\|JWB-0028103	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	02/26/08	02/26/08	129	Genomic	unknown
ss97927620	HUMANGENOME_JCVI\|1103675056164	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgaggaagaagagcatta	03/30/08	03/30/08	130	Genomic	unknown
ss108085070	1000GENOMES\|CEU.trio.12.15.2008_36743_chr1_29415224	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	12/15/08	12/15/08	130	Genomic	unknown
ss110226778	1000GENOMES\|NA19240_2008_12_16_35340_chr1_29415224	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	12/16/08	12/17/08	130	Genomic	unknown
ss118587617	ILLUMINA-UK\|NA18507_000034829_NCBI36.1_chr1_29415224	rev/T	A/G	tccctccaacagcaggcagttcaggaagga	tccgtagtttcctgagggagaagagcatta	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 ATTCCTCCTC AGGTGTGGGT GTGAAATGCC TGTGATTAGC AGCAGCTGTT CTCCAGATGA
 GCCGTCTGCA GGCTGTGTCA GCCCTGTCTG GCCTCCCTTT TCTGGAATGT GTGGCTTTTT
 GAGAAGATTG CAGTGGGGAG TAAACTAAGC ATTGTGAAGT GCCTGCGACA TGCTGGTTTC
 ATTTCATATG TTACCTGATT TTCATGATAA CCATGAACAC TAAAGAATAT TGTCCCCCTA
 TACAGACAAG CAAGCTAAGG CTCAGAGGTT GGTTAGGCAG ACAGTCCAAA GCAGAGCCCA
 GATCAGGCCT AGGATGGCGT GGACTCAAGT CCATGCTCTT TCACTGCCCA AACATCACTG
 GTTGACCCTT TAATGCTCTT CTCCCTCAGG AAACTACGGA
 Y
 TCCTTCCTGA ACTGCCTGCT GTTGGAGGGA ACGAAGGTGT TGCACAGGTG GTAGCGGTGG
 GCAGCAATGT GACCGGGCTG AAGCCAGGAG ACTGGGTGAT TCCAGCAAAT GCTGGTTTAG
 GTGAGTTTCT CCAGGTGTCA GCTGCCTATT CGTTCTTCCA GATCCTATTT CACCCACTCT
 GTCGGCATCC ACTGATTGGC CGAGTGTACC TGGGTAATGC AGGGTTTATT TTTTTTATTT
 ATTTATTTAT TTTGAGACGG AGTTTTGCTC TTATTGCCCA GGCTGGAGTG CAATGGCGCG
 ATCTCAGCTC ACCAAAACCT CCGCCTCCCC AGTTCAAGTG ATTCTCCTGC CTCAGCCTCC
 CAAGTAGCTG GGATTACAGG CGCCTACCAC CACGCCCGGC

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_004610.18 AA393871 ABBA01035081 AC025145 BC001419 Hs.19513

dbSNP Blast Analysis

UniGene Cluster ID
183646

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss19124444	CEPH		184	AF					0.850	0.150

ss24150391	AFD_EUR_PANEL	European	48	IG	0.833	0.167		0.752	0.917	0.083

	AFD_AFR_PANEL	African American	34	IG	0.588	0.353	0.059	1.000	0.765	0.235

	AFD_CHN_PANEL	Asian	48	IG	0.333	0.500	0.167	1.000	0.583	0.417

ss41288357	HapMap-CEU	European	120	IG	0.733	0.233	0.033	0.527	0.850	0.150

	HapMap-HCB	Asian	88	IG	0.182	0.614	0.205	0.100	0.489	0.511

	HapMap-JPT	Asian	84	IG	0.357	0.310	0.333	0.020	0.512	0.488

	HapMap-YRI	Sub-Saharan African	120	IG	0.467	0.433	0.100	1.000	0.683	0.317

ss48422184	AGI_ASP population	multiple	76	IG	0.763	0.211	0.026	0.655	0.868	0.132

ss4924063	JBIC-allele		1498	AF					0.527	0.473

ss68762156	HapMap-CEU	European	120	GF	0.733	0.233	0.033		0.850	0.150

	HapMap-HCB	Asian	90	GF	0.200	0.600	0.200		0.500	0.500

	HapMap-JPT	Asian	90	GF	0.356	0.311	0.333		0.511	0.489

	HapMap-YRI	Sub-Saharan African	120	GF	0.467	0.433	0.100		0.683	0.317

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss24150391	71
ss48422184	39	29	8	1
ss68762156	269
ss76890942	1206
ss97927620	1

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs1128400	1303	29	8	1

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5151	ss68762156	G/G	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	chr1-HapMap-HCB
5151	ss76890942	A/G	CSHL-HAPMAP	HapMap-HCB	NA18558	CH18558	r27_ch1_CHB_illumina:human_1m_beadchip

Genotype data submitted for	1318	samples from	1303	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 .