Reference SNP(refSNP) Cluster Report: rs1145231

Reference SNP(refSNP) Cluster Report: rs1145231

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

HGVS Names
NG_008648.1:g.75369T>C
NM_000534.3:c.1181T>C
NM_000534.4:c.1181T>C
NM_001128143.1:c.1064T>C
NM_001128144.1:c.1181T>C
NP_000525.1:p.Met394Thr
NP_001121615.1:p.Met355Thr
NP_001121616.1:p.Met394Thr
NT_005403.16:g.40928596T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48421248 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1145231 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
ss1803641	KWOK\|OVLP-000925-663355	fwd/B	C/T	atacttcagtcattccattccaaaatgata	gcataatgatgaatctggaaaaaacactga	10/05/00	10/10/03	87	Genomic	99 %
ss1842174	KWOK\|OVLP-000925-661967	fwd/B	C/T	atacttcagtcattccattccaaaatgata	gcataatgatgaatctggaaaaaacactga	10/05/00	10/10/03	87	Genomic	97 %
ss3626281	SC_JCM\|AC013468.11_71585	rev/T	A/G	tcagtgttttttccagattcatcattatgc	tatcattttggaatggaatgactgaagtat	09/24/01	10/10/03	100	Genomic	unknown
ss48421248	APPLERA_GI\|hCV1044135	rev/T	A/G	tcagtgttttttccagattcatcattatgc	tatcattttggaatggaatgactgaagtat	09/28/05	11/03/06	126	Genomic	unknown
ss68838588	PERLEGEN\|PGP04766685	fwd/B	C/T	atacttcagtcattccattccaaaatgata	gcataatgatgaatctggaaaaaacactga	01/30/07	08/14/07	127	Genomic	unknown
ss74821797	AFFY\|SNP_M-326233	fwd/B	C/T	atacttcagtcattccattccaaaatgata	gcataatgatgaatctggaaaaaacactga	08/09/07	08/09/07	128	Genomic	unknown
ss74903674	ILLUMINA\|ILMN_Human_1M_rs1145231	fwd/B	C/T	atacttcagtcattccattccaaaatgata	gcataatgatgaatctggaaaaaacactga	08/28/07	08/29/07	129	Genomic	unknown
ss76862601	CGM_KYOTO\|2653	fwd/B	C/T	atacttcagtcattccattccaaaatgata	gcataatgatgaatctggaaaaaacactga	09/12/07	09/12/07	129	cDNA	unknown

Fasta sequence (Legend)

 TTGTTTATAT TTATCTTTTT TATTATTTAA AATCTTGTCT ATTATTTTCA TAATTTCCCC
 TAACATTTGT TAATTTGTAT TTTTAGGAAT CTGTTTTAAT TGCTCTTGAA AATCTGATGA
 CGACTTGTTA TGGACCATTA CCTAGTACAA ATTCTTATGA AAATAATAAA ACAGATGTTT
 CCGCAGCTGA CATCGTTCTT AGTAAAACAG CAGAAACAGA TGTGCTTTTT AATAAAGTGG
 AATCATCTGG AAAGAATTAT TCAAATGTTG ATACTTCAGT CATTCCATTC CAAAATGATA
 Y
 GCATAATGAT GAATCTGGAA AAAACACTGA TGATTGTTTA AATCACCAGA TAAGTATTGG
 TGACTTTGGT TATGGTCATT GTAGTAGTGA AATTTCTAAC ATTGATAAAA ACACTAAGAA
 TGCATTTCAG GACATTTCAA TGAGTAATGT ATCATGGGAG AACTCTCAGA CGGAATATAG
 TAAAACTTGT TTTATAAGTT CCGTTAAGCA CACCCAGTCA GAAAATGGCA ATAAAGACCA
 TATAGATGAG AGTGGGGAAA ATGAGGAAGA AGCAGGTCTT GAAAACTCTT CGGAAATTTC

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_005403.15 AC008122 AC013468.7 AC019178 AC019178.2

dbSNP Blast Analysis

UniGene Cluster ID
111749

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1803641	CEPH		184	AF						1.000

ss1842174	SC_12_A	Asian	18	IG			1.000			1.000

	SC_12_AA	African American	24	IG		0.083	0.917	1.000	0.042	0.958

	SC_12_C	European	14	IG			1.000			1.000

ss48421248	HapMap-CEU	European	116	IG			1.000			1.000

	HapMap-HCB	Asian	88	IG			1.000			1.000

	HapMap-JPT	Asian	86	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	116	IG		0.121	0.879	0.752	0.060	0.940

	AGI_ASP population	multiple	70	IG	0.029	0.029	0.943	0.001	0.043	0.957

ss68838588	HapMap-CEU	European	120	GF			1.000			1.000

	HapMap-HCB	Asian	90	GF			1.000			1.000

	HapMap-JPT	Asian	90	GF			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.100	0.883		0.067	0.933

Concordant Genotype	Total Sample	C/T	T/T
ss1842174	36	1	32
ss48421248	906
ss68838588	269	9	260

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs1145231	941		10	290

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5297	ss48421248	A/G	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	r27_ch2_YRI_bcm:genotype_0002	1858640
5297	ss68838588	C/C	CSHL-HAPMAP	HapMap-YRI	NA19223	YOR058.03	chr2-HapMap-YRI

Genotype data submitted for	943	samples from	941	individuals	Individual with multiple genotypes submission:	270

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 .