Reference SNP(refSNP) Cluster Report: rs12572

Reference SNP(refSNP) Cluster Report: rs12572

refSNP ID: rs12572
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	52/129
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_152464.1:c.472G>A
NP_689677.1:p.V158I
NT_010799.14:g.1424804G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48426336 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12572 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
ss14855	CGAP-GAI\|59485	rev/B	C/T	ttccaaggtaagtgcagacgaaggcagcaa	caccgtgacaatgaaattgaagatggtgat	08/23/99	10/10/03	52	cDNA	99 %
ss1533065	LEE\|595671	fwd/T	A/G	atcaccatcttcaatttcattgtcacggtg	ttgctgccttcgtctgcacttaccttggaa	09/13/00	10/10/03	86	cDNA	unknown
ss4396607	LEE\|ge595671	fwd/T	A/G	atcaccatcttcaatttcattgtcacggtg	ttgctgccttcgtctgcacttaccttggaa	04/25/02	10/10/03	106	cDNA	unknown
ss4422003	LEE\|e595671	fwd/T	A/G	atcaccatcttcaatttcattgtcacggtg	ttgctgccttcgtctgcacttaccttggaa	04/26/02	10/10/03	106	cDNA	unknown
ss16225494	CGAP-GAI\|1458590	fwd/T	A/G	atcaccatcttcaatttcattgtcacggtg	ttgctgccttcgtctgcacttaccttggaa	11/18/03	11/22/03	120	cDNA	unknown
ss48426336	APPLERA_GI\|hCV7442521	fwd/T	A/G	atcaccatcttcaatttcattgtcacggtg	ttgctgccttcgtctgcacttaccttggaa	09/28/05	11/03/06	126	Genomic	unknown
ss69194031	PERLEGEN\|PGP04690313	fwd/T	A/G	atcaccatcttcaatttcattgtcacggtg	ttgctgccttcgtctgcacttaccttggaa	01/30/07	08/14/07	127	Genomic	unknown
ss74864515	ILLUMINA\|ILMN_Human_1M_rs12572	fwd/T	A/G	atcaccatcttcaatttcattgtcacggtg	ttgctgccttcgtctgcacttaccttggaa	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 GCTGCTTCTA TTCTGAATCA TCTTCTTTTT CTTTTTCCCA GGATACAAGA CATGGTGGGA
 CTCTCAGCGA CCTGGGAAAG CAAGGTGAGG TACTAGGAGA TCAGGCTTCT AAAACCTTTT
 CCTGAGATGG GTCATGACAC TCAGGCTTGT TGTTTGACTG AAACCCAGTT GGTGGGGGAG
 CCATGAGATA AGAGCACCTC CTAGAGAATG TTGAACTAAA GGTGCCCTCT CTGGCTCCTC
 CCCAAAGTGA GATCATTGAA GGCTCTGGTC ATCACCATCT TCAATTTCAT TGTCACGGTG
 R
 TTGCTGCCTT CGTCTGCACT TACCTTGGAA GCCAATATAT CTTCACAGAA ATGGCCTCGG
 TGAGTAGGCA CTGGGCAGGG CAGGGTGCCC CTGGTGGGGG TGTTAGTGGG TAAGGGAGGA
 CGTATGTGAA AGTGCCTTGC ACAGGTTAGG TATTGAACAG ATATTTATGC CATTAATAAG
 GGGAGCATTA GAGCTTTCCA GCAGTCACGG GAGGTTAGGT AATAACCCCA GGAGAAGCCA
 CATTCTCTTT TCTTCCCCTC CCCCAACTTA GAGGGTGGTT GGGGGGCTCT CCATCCTCAT

GeneView

GeneView via analysis of contig annotation: TMEM199 transmembrane protein 199

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_010799->NM_152464

function

HuRef

NW_001838430->NM_152464

function

Celera

NW_926750->NM_152464

function

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


reference	NT_010799->NM_152464->NP_689677	1424805	forward	479	missense	A	Ile [I]	1	158
					contig reference	G	Val [V]	1	158

HuRef	NW_001838430->NM_152464->NP_689677	3710103	reverse	479	missense	A	Ile [I]	1	158
					contig reference	G	Val [V]	1	158

Celera	NW_926750->NM_152464->NP_689677	1416037	forward	479	missense	A	Ile [I]	1	158
					contig reference	G	Val [V]	1	158

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12572 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838430.2	3710103	22896218	minus	C	alt_assembly_8	HuRef	HuRef	view	300
17	NW_926750.1	1416037	23549567	plus	G	alt_assembly_1	Celera	Celera	view	300
17	NT_010799.14	1424805	23711938	plus	G	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
R34521 AA576765 AI057135 Hs.125035

dbSNP Blast Analysis
GenBank HTGS Finished:
AC002094.1 NC_000017.9

UniGene Cluster ID
368878

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1533065	CEPH		184	AF						1.000

ss48426336	AGI_ASP population	African American	78	IG	0.026	0.179	0.795	0.479	0.115	0.885

ss69194031	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	0.050	0.300	0.650		0.200	0.800

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.124+/-0.216	309	249	0	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 .