Reference SNP(refSNP) Cluster Report: rs34907038

Reference SNP(refSNP) Cluster Report: rs34907038

refSNP ID: rs34907038
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	126/129
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_022754.4:c.796C>T
NP_073591.2:p.P266S
NT_023133.12:g.19758528C>T

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss48412792 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs34907038 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
ss48412792	APPLERA_GI\|hCV25931556		fwd/T	A/G	accagaagccaactaacccaacttgaatgg	tgcactcatccatgggaacctctgtgttga	09/28/05	11/03/06	126	Genomic			unknown
ss68960342	PERLEGEN\|PGP17793123		rev/B	C/T	tcaacacagaggttcccatggatgagtgca	ccattcaagttgggttagttggcttctggt	01/30/07	01/30/07	127	Genomic			unknown

Fasta sequence (Legend)

 TGTTTGTGTA AGTTTTATTA CCTAGGATTG CCAAAATAAT GAAAAAGTCA CAGAGACAAC
 AATTTAAAAA AGAATCACAC GAATAGCCCC CCATGTTGTA GGTTTCTCTA AAGACAGTTT
 ACTTCTATTT AATTATTTGG GGCCATGCAT TCCAGATGTT CTGAGATGGC CTCATTTTCA
 AAATTTGTAT CCCATATTAC CCAGTCACCT TTCATACGCT GTGTATTTAT ATTTTAAAAG
 AAATTAATTA TGTAAAAGTA ATTTCTACTC ACCAGAAGCC AACTAACCCA ACTTGAATGG
 R
 TGCACTCATC CATGGGAACC TCTGTGTTGA GAAATAAATG GCTTTGAATA CTTTTTATAC
 AGGGTCTTAG AGGCAATATC TTCTGATTAA CTGGAAGGAA CCTCTCACCA CATTTCAAGA
 TTCAGATAGA ACATGGTTAG TGAAATTTGG GGGAAATGCT GCAACAAGGG TGTTAGCCTA
 ACTTCCTGTA ACCTTCTTTG ATCTGTAAAT CAGCACACAC GCAAAGATCA AGTGGCTTCT
 ATTTTTCCTC CCAGTCCCCC ATTTAATCTG AGCACTGCTT GGGTATATAA TGGAGGTGGG

GeneView

GeneView via analysis of contig annotation: SFXN1 sideroflexin 1

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_023133->NM_022754

function

HuRef

NW_001838954->NM_022754

function

Celera

NW_922784->NM_022754

function

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


reference	NT_023133->NM_022754->NP_073591	19758529	forward	865	missense	T	Ser [S]	1	266
					contig reference	C	Pro [P]	1	266

HuRef	NW_001838954->NM_022754->NP_073591	414249	reverse	865	missense	T	Ser [S]	1	266
					contig reference	C	Pro [P]	1	266

Celera	NW_922784->NM_022754->NP_073591	48615961	forward	865	missense	T	Ser [S]	1	266
					contig reference	C	Pro [P]	1	266

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs34907038 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_001838954.2	414249	170048076	plus	G	alt_assembly_8	HuRef	HuRef	view	300
5	NW_922784.1	48615961	170987945	minus	C	alt_assembly_1	Celera	Celera	view	300
5	NT_023133.12	19758529	174881549	minus	C	ref_assembly	reference	reference	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000005.8

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):
NM_022754.4

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/G	G/G	HWP	A	G
ss48412792	AGI_ASP population	multiple	78	IG	0.051	0.949	1.000	0.026	0.974

ss68960342	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		1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.012+/-0.076	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 .