Reference SNP(refSNP) Cluster Report: rs12257132

Reference SNP(refSNP) Cluster Report: rs12257132

refSNP ID: rs12257132
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_001010863.1:c.248C>T
NP_001010863.1:p.P83L
NT_017696.14:g.1178295G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss18646463 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12257132 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
ss18646463	SC_SNP\|SC-CHR9-12_NA17119-200402.chr10.NT_017696.14_1178296	fwd/T	A/G	tgaccttaccttggggctctcttctttagc	ggatggtgtctaaacagagaaagccgggca	02/20/04	10/26/06	120	Genomic	unknown
ss67169731	ILLUMINA\|HumanHap650Yv1.0_rs12257132	fwd/T	A/G	tgaccttaccttggggctctcttctttagc	ggatggtgtctaaacagagaaagccgggca	11/14/06	11/14/06	127	Genomic	unknown
ss69078347	PERLEGEN\|PGP04785347	fwd/T	A/G	tgaccttaccttggggctctcttctttagc	ggatggtgtctaaacagagaaagccgggca	01/30/07	03/31/08	127	Genomic	unknown
ss71099930	ILLUMINA\|HumanHap650Yv3.0_rs12257132	fwd/T	A/G	tgaccttaccttggggctctcttctttagc	ggatggtgtctaaacagagaaagccgggca	04/23/07	04/23/07	127	Genomic	unknown
ss74818401	AFFY\|SNP_M-317696	fwd/T	A/G	tgaccttaccttggggctctcttctttagc	ggatggtgtctaaacagagaaagccgggca	08/09/07	08/09/07	128	Genomic	unknown
ss75387912	ILLUMINA\|ILMN_Human_1M_rs12257132	fwd/T	A/G	tgaccttaccttggggctctcttctttagc	ggatggtgtctaaacagagaaagccgggca	08/28/07	08/29/07	129	Genomic	unknown
ss76630602	AFFY\|AFFY_6_1M_SNP_A-8491917	rev/B	C/T	tgtttagacaccatcc	gctaaagaagagagcc	08/28/07	08/30/07	129	Genomic	unknown
ss86267304	CORNELL\|hCV25988300	fwd/B	C/T	tgaccttaccttggggctctcttctttagc	ggatggtgtctaaacagagaaagccgggca	01/21/08	01/21/08	129	Genomic	unknown

Fasta sequence (Legend)

 ACCTGCCCAC TGGTCCAGAG GAGGAGAGAG TGTAAGGAGG GGACCACGAG GTGCATTCTA
 GTCACCTAGA AAGCATGCCA GAGTGCAGAG AAGGCTGGGG ATGACAGGCA AGGGAGTGGC
 ACGGTCAAGA CAGGAGAGAA CACGATACCT CTCCCTGACT GTGTGGGCAG TGACCTTACC
 TTGGGGCTCT CTTCTTTAGC
 R
 GGATGGTGTC TAAACAGAGA AAGCCGGGCA TTAGGAAGGG GGTCGTGTGA CAAGAGGTGC
 AGAGCATTCC CTAGAGCTTT CACCTCCCTC TCCTTGGTCC TCTCACTCAC GGTTGCCCTC
 GAGAGACCCG GGGCCTGGCT GCTATGTGAT GAAGAGGCTG TTTCCTCCCC TTATTTGTGG
 GGATACACAA GGATAAGCAA

GeneView

GeneView via analysis of contig annotation: C10orf128 chromosome 10 open reading frame 128

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_017696->NM_001010863

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_017696->NM_001010863->NP_001010863	1178296	reverse	274	missense	T	Leu [L]	2	83
					contig reference	C	Pro [P]	2	83

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12257132 maps exactly once on NCBI human chromosome 10

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
10	NW_924685.1	1001574	43959420	plus	G	alt_assembly_1	Celera	Celera	view	200
10	NW_001837975.2	699008	44638555	minus	C	alt_assembly_8	HuRef	HuRef	view	200
10	NT_017696.14	1178296	50043838	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_017696

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_001010863.1

UniGene Cluster ID
385493

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss18646463	HapMap-CEU	European	120	IG		0.017	0.983	1.000	0.008	0.992

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	90	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.350	0.567	0.527	0.258	0.742

ss69078347	HapMap-CEU	European	120	GF		0.017	0.983		0.008	0.992

	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	0.083	0.350	0.567		0.258	0.742

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.141+/-0.225	270	210	270	0

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 .