Reference SNP(refSNP) Cluster Report: rs3136819

Reference SNP(refSNP) Cluster Report: rs3136819

refSNP ID: rs3136819
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	103/129
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_001641.2:c.440-61C>T
NM_080648.1:c.440-61C>T
NM_080649.1:c.440-61C>T
NT_026437.11:g.1924929C>T

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss4385210 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3136819 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
ss4385210	EGP_SNPS\|APEX-002508	fwd/B	C/T	accaattgctaattctctatctctgcccca	ctcttgattgctttcccttttcttatagtt	03/18/02	04/07/04	103	Genomic	unknown
ss5586243	SNP500CANCER\|APEX1-05	fwd/B	C/T	accaattgctaattytctatctctgcccca	ctcttgattgctttcccttttcttatagtt	09/26/02	04/07/04	116	Genomic	unknown
ss66863141	EGP_SNPS\|APEX_002508	fwd/B	C/T	accaattgctaattytctatctctgcccca	ctcttgattgctttcccttttcttatagtt	11/09/06	03/31/08	127	Genomic	unknown
ss76861197	CGM_KYOTO\|1249	fwd/B	C/T	accaattgctaattctctatctctgcccca	ctcttgattgctttcccttttcttatagtt	09/12/07	09/12/07	129	cDNA	unknown

Fasta sequence (Legend)

 AGGAAGAAGC CCCAGATATA CTGTGCCTTC AAGAGACCAA ATGTTCAGAG AACAAACTAC
 CAGCTGAACT TCAGGAGCTG CCTGGACTCT CTCATCAATA CTGGTCAGCT CCTTCGGACA
 AGGAAGGGTA CAGTGGCGTG GGCCTGCTTT CCCGCCAGTG CCCACTCAAA GTTTCTTACG
 GCATAGGTGA GACCCTATTG ATGCCTAATG CCTGAACTCT TCAAAACCAA TTGCTAATTC
 TCTATCTCTG CCCCA
 Y
 CTCTTGATTG CTTTCCCTTT TCTTATAGTT TTTTATGCTA ATTCTGTTTC ATTTCTATAG
 GCGATGAGGA GCATGATCAG GAAGGCCGGG TGATTGTGGC TGAATTTGAC TCGTTTGTGC
 TGGTAACAGC ATATGTACCT AATGCAGGCC GAGGTCTGGT ACGACTGGAG TACCGGCAGC
 GCTGGGATGA AGCCTTTCGC AAGTTCCTGA AGGGCCTGGC TTCCCGAAAG CCCCTTGTGC
 TGTGTGGAGA CCTCA

GeneView

GeneView via analysis of contig annotation: APEX1 APEX nuclease (multifunctional DNA repair enzyme) 1

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

GeneView via analysis of contig annotation: TMEM55B transmembrane protein 55B

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_026437->NM_001641

function

reference

NT_026437->NM_080648

function

reference

NT_026437->NM_080649

function

reference

NT_026437->NM_001100814

function

reference

NT_026437->NM_144568

function

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


reference	NT_026437->NM_001641->NP_001632	1924929	forward	intron

reference	NT_026437->NM_080648->NP_542379	1924929	forward	intron

reference	NT_026437->NM_080649->NP_542380	1924929	forward	intron

reference	NT_026437->NM_001100814->NP_001094284	1924929	reverse	3' near gene

reference	NT_026437->NM_144568->NP_653169	1924929	reverse	3' near gene

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs3136819 maps exactly once on NCBI human chromosome 14

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
14	NW_925539.1	728361	786239	plus	C	alt_assembly_1	Celera	Celera	view	255
14	NW_001838110.1	735532	1046708	plus	C	alt_assembly_8	HuRef	HuRef	view	255
14	NT_026437.11	1924929	19994929	plus	C	ref_assembly	reference	reference	view	255

NCBI Resource Links

Submitter-Referenced
GenBank
NT_037845.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AL355075.6

UniGene Cluster ID
73722

Population Diversity

	Sample Ascertainment				Genotype Detail			Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	HWP	C	T
ss4385210	PDR90	Global	152	IG	0.961	0.039	1.000	0.980	0.020

ss5586243	P1		200	GF	0.970	0.030	1.000	0.985	0.015

	CAUC1		62	GF	1.000			1.000

	AFR1		48	GF	0.917	0.083	1.000	0.959	0.042

	HISP1		44	GF	0.955	0.045	1.000	0.978	0.023

	PAC1		46	GF	1.000			1.000

ss66863141	HSP_GENO_PANEL		120	IG	0.983	0.017	1.000	0.992	0.008

	CEU_GENO_PANEL	European	116	IG	1.000			1.000

	AAM_GENO_PANEL	African American	102	IG	0.922	0.078	1.000	0.961	0.039

	CHB_GENO_PANEL	Asian	82	IG	1.000			1.000

	YRI_GENO_PANEL	Sub-Saharan African	100	IG	0.940	0.060	1.000	0.970	0.030

	JPT_GENO_PANEL	Asian	90	IG	1.000			1.000

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.029+/-0.116	422	422	0	0

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	YES

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Revised: May 25, 2006 1:38 PM .