Reference SNP(refSNP) Cluster Report: rs1048774

Reference SNP(refSNP) Cluster Report: rs1048774

refSNP ID: rs1048774
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/129
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_001077516.1:c.189C>T
NM_006979.2:c.189C>T
NP_001070984.1:p.G63G
NP_008910.2:p.G63G
NT_007592.14:g.24027460C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss4189136 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1048774 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss1521953	LEE\|330931		fwd/B	C/T	tttccaccatggtcacagccatgcccatgg	catggccacactcacgagagcatctggcat	09/13/00	10/10/03	86	cDNA			unknown
ss4189136	SC_JCM\|AF120161.1_288		rev/T	A/G	atgccagatgctctcgtgagtgtggccatg	ccatgggcatggctgtgaccatggtggaaa	10/15/01	10/10/03	101	Genomic			unknown

Fasta sequence (Legend)

 CTGGTCAGCG TGATGGCCAG AGGCCTGGGG GGCCCCCACT GGGTGGCCGT GGGACTGCTG
 ACCTGGGCGA CCTTGGGGCT TCTGGTGGCT GGACTCGGGG GTCATGACGA CCTGCACGAC
 GATCTGCAAG AGGACTTCCA TGGCCACAGC CACAGGCACT CACATGAAGA TTTCCACCAT
 GGTCACAGCC ATGCCCATGG
 Y
 CATGGCCACA CTCACGAGAG CATCTGGCAT GGACATACCC ACGATCACGA CCATGGACAT
 TCACATGAGG ATTTACACCA TGGCCATAGC CATGGCTACT CCCATGAGAG CCTCTACCAC
 AGAGGACATG GACATGACCA TGAGCATAGC CATGGAGGCT ATGGGGAGTC TGGGGCTCCA
 GGCATCAAGC AGGACCTGGA

GeneView

GeneView via analysis of contig annotation: SLC39A7 solute carrier family 39 (zinc transporter), member 7

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_007592->NM_001077516

function

reference

NT_007592->NM_006979

function

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


reference	NT_007592->NM_001077516->NP_001070984	24027461	forward	306	synonymous	T	Gly [G]	3	63
					contig reference	C	Gly [G]	3	63

reference	NT_007592->NM_006979->NP_008910	24027461	forward	609	synonymous	T	Gly [G]	3	63
					contig reference	C	Gly [G]	3	63

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1048774 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838980.1	6183565	32911256	plus	C	alt_assembly_8	HuRef	HuRef	view	200
6	NT_113891.1	4549372	33237915	plus	C	alt_assembly_3	c6_COX	c6_COX	view	200
6	NT_113897.1	381428	33240890	plus	C	alt_assembly_4	c6_QBL	c6_QBL	view	200
6	NT_007592.14	24027461	33277189	plus	C	ref_assembly	reference	reference	view	200
6	NW_923073.1	6187898	34723577	plus	C	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AL031228 AL031228 Hs.66776

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:	GenBank mRNA:
NM_001077516.1 NM_006979.2 NM_021976.3	AL031228.1 AL645940.4 AL662824.9 AL844527.6 CR354565.6 CR759733.4 CR936877.4 D84401.1	CR388385.3 CR753824.2 CR847784.4 CR847805.4	BC000645.2 D82060.1

UniGene Cluster ID
278721

Population Diversity

There is no frequency data.

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 .