Reference SNP(refSNP) Cluster Report: rs9933960

Reference SNP(refSNP) Cluster Report: rs9933960

refSNP ID: rs9933960
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	C/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_001008274.2:c.391-956G>C
NT_010393.15:g.22542539G>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss13773027 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs9933960 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
ss13773027	BCM_SSAHASNP\|chr16.NT_024812.10_2629127		fwd/T	C/G	tgtgccaagctctgtgcctgcctgtctggt	ggagagaccaaaccacactgatgtttgtca	11/05/03	11/22/03	119	Genomic			unknown

Fasta sequence (Legend)

 CTGCCCCCTA CTCCAAGCCC ATGTGTGTAC AGGCAGGCTG ACTTGGTGGT CAGGCTGACA
 GGCTGACTGA GGCTGATGTT CTGCTTTTAA GTAAGAGAGG AAGCCCAGGA GTAGGGGTAG
 GTTGCCTTTC TTCTTTCATA TATCCTTCAT GTACCCCCTG AGGTCTGTTG TGTGCCAAGC
 TCTGTGCCTG CCTGTCTGGT
 S
 GGAGAGACCA AACCACACTG ATGTTTGTCA TCCTCGCAAA GACCTGTGCT ATGGGGCTGA
 CTGCTGAGCA GAGGGGATCA GGGAAGGCAA GGCCAGGGAG GGGTCAACAA AACAGACAAG
 GGGCTGGggg tgtggcggtt catgcctgta atcccagcat gctgggaggc tgaggtggga
 ggattgcttg aggccaggag ttggagacca gtctgggcaa tatagtgaga ttgtctctac
 aaaaaTATTT TAAAAAATCA Tggccaggag tggtggctca tgtctaatcc cagcacttcg
 ggaggctgac gtgggtggat cacctgaggt cagaagtttg agaccagcct ggccaacatg
 gtgaaaccct gtctctacta aaaataccaa aattagccag gcgtggtggt gcaccaaaat
 tagtcccagc tacttgggag gctgaggcag gagaatcgct tgaacccagg aggtggaggt
 tgcagtgagc tgagattgtg

GeneView

GeneView via analysis of contig annotation: TRIM72 tripartite motif-containing 72

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: PYDC1 PYD (pyrin domain) containing 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_010393->NM_001008274

function

HuRef

NW_001838236->NM_001008274

function

Celera

NW_926306->NM_001008274

function

Celera

NW_926306->NM_152901

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_010393->NM_001008274->NP_001008275	22542539	forward	intron

HuRef	NW_001838236->NM_001008274->NP_001008275	909291	forward	intron

Celera	NW_926306->NM_001008274->NP_001008275	721938	reverse	intron

Celera	NW_926306->NM_152901->NP_690865	721938	forward	5' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs9933960 maps exactly once on NCBI human chromosome 16

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
16	NW_001838236.1	909291	28791089	plus	G	alt_assembly_8	HuRef	HuRef	view	200
16	NW_926306.1	721938	29068568	minus	C	alt_assembly_1	Celera	Celera	view	200
16	NT_010393.15	22542539	31136961	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_024812

dbSNP Blast Analysis
GenBank HTGS Finished:
AC009088.9 NC_000016.8

Population Diversity

	Sample Ascertainment				Genotype Detail		Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	HWP	G
ss13773027	HapMap-CEU	European	112	IG	1.000		1.000

	HapMap-HCB	Asian	88	IG	1.000		1.000

	HapMap-JPT	Asian	84	IG	1.000		1.000

	HapMap-YRI	Sub-Saharan African	112	IG	1.000		1.000

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