Reference SNP(refSNP) Cluster Report: rs162913

Reference SNP(refSNP) Cluster Report: rs162913

refSNP ID: rs162913
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

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

HGVS Names
NM_015577.1:c.167+3533C>A
NT_006576.15:g.34733993C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1696358 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs162913 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
ss239409	KWOK\|OVLP-000621-328585	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	06/30/00	10/10/03	87	Genomic	94 %
ss242792	KWOK\|OVLP-000621-358995	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	06/30/00	10/10/03	79	Genomic	93 %
ss427297	KWOK\|OVLP-000621-318034	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	06/30/00	10/10/03	79	Genomic	99 %
ss429094	KWOK\|OVLP-000621-322565	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	06/30/00	10/10/03	87	Genomic	99 %
ss637891	SC_JCM\|AC026801.2_45461	rev/B	G/T	atgtgggccttagttttattatctgcaaaa	ggaggtggtgactcttacctaactgctatg	07/12/00	10/10/03	87	Genomic	unknown
ss909041	KWOK\|OVLP-000804-189914	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	09/01/00	10/10/03	86	Genomic	99 %
ss912579	KWOK\|OVLP-000804-205954	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	09/01/00	10/10/03	86	Genomic	99 %
ss915401	KWOK\|OVLP-000804-217419	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	09/01/00	10/10/03	86	Genomic	99 %
ss1059135	KWOK\|OVLP-000804-199907	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	09/02/00	10/10/03	86	Genomic	93 %
ss1694184	KWOK\|OVLP-000925-381536	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	10/05/00	10/10/03	87	Genomic	99 %
ss1695613	KWOK\|OVLP-000925-398119	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	10/05/00	10/10/03	87	Genomic	99 %
ss1696358	KWOK\|OVLP-000925-406147	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	10/05/00	10/10/03	87	Genomic	99 %
ss1752120	KWOK\|OVLP-000925-392197	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	10/05/00	10/10/03	87	Genomic	93 %
ss5318664	TSC-CSHL\|TSC1614187	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	09/20/02	10/10/03	108	Genomic	unknown
ss5328821	TSC-CSHL\|TSC1589201	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	09/20/02	10/10/03	108	Genomic	unknown
ss5496402	TSC-CSHL\|TSC0507884	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	09/21/02	10/10/03	108	Genomic	unknown
ss5507227	TSC-CSHL\|TSC0578435	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	09/21/02	10/10/03	108	Genomic	unknown
ss5520314	TSC-CSHL\|TSC0529027	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	09/21/02	10/10/03	108	Genomic	unknown
ss10246384	BCM_SSAHASNP\|chr5.NT_006576.13_17187429	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	06/27/03	10/10/03	116	Genomic	unknown
ss14637206	WI_SSAHASNP\|chr5.NT_006576.14_17213342	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	11/05/03	11/22/03	119	Genomic	unknown
ss44630799	ABI\|hCV1003295	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	07/19/05	07/19/05	126	Genomic	unknown
ss77798494	HGSV\|Cor12156_SNV_20070510.chr5_34796993	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	10/09/07	10/14/07	129	Genomic	unknown
ss85928416	HGSV\|Cor19129_SNV_20070510.chr5_34796993	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	12/06/07	12/10/07	130	Genomic	unknown
ss108952396	1000GENOMES\|CEU.trio.12.15.2008_1242658_chr5_34796993	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	12/15/08	12/16/08	130	Genomic	unknown
ss111682251	1000GENOMES\|NA19240_2008_12_16_1113348_chr5_34796993	fwd/T	A/C	catagcagttaggtaagagtcaccacctcc	ttttgcagataataaaactaaggcccacat	12/16/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 TTCATGTCAT CCCAGAGAAA GGGGAGAGAA AGGTTTATGA TAATTTTGTC CAAGATAGTA
 CTTACTAAAG AGAAGACAGA AAATTTAGAT GAGCAGCTTA GCTACAATTG TGATCACCTT
 AACAAATTTG AACCTTTTGA TCATAAGATA TTTATTACAT GTGttctctt tatttattgt
 ggtaaaatgc gtataacata aaatttacca ttttaaccat tttaaagtat acaatgtaga
 ggcattaagt atattcacaa tgttgcacaa ccattgtcac tttctagttc tagaactttc
 taatcaaccc aaagaaaacc ccgaacccat tagggagaaa ctccccaacc tcccctcccc
 ttcctctggc aaccatgaat ctgggttctg tctctggatt tgtctgctct ggatattttt
 tataaatgta atcatataat atgtggcctc ttgtctctgt tcctttcact tagcataatg
 ttttcaaggc tcacccgagt tgtagcttct gtcagtactt cattctattc tctcttcatg
 gTAGACATAT ACATAGCAGT TAGGTAAGAG TCACCACCTC C
 M
 TTTTGCAGAT AATAAAACTA AGGCCCACAT AACACAGCTC TTCCTGAATT TACCTTTTTG
 TGTGCATGTG TGtgagacag ggtctcactc tgtcacccag gctggaatgc agtggtgcag
 tcaccgctca ctgtagcctc aacctcacag ggtcaagtga tcctcctgcc tcagcctctc
 aattagctgg gactacaggt atgcaccact gcacccagct aattttggtt ttgttttgtt
 ttgttttgtt tttgtaatga tggggtcttg ctgtcttgtc ctagtgatcc tcccatgtca
 gcttcccaaa gtgttgggat tacaggcatg agccaccatt cccagccTTC TATTTTCTAG
 AGAGCTTTCG TGGTAATTTT GCGCTGGAAT CTACAGTTGC CTGTCTGTCT AGAGGCTTGA
 TTTTGGCCTT CAAGGTCTTT CCTCTGGCTC TGCCCCACTT ACCTACATCC TGTCTCCCCG
 CTGTTTCTTC T

GeneView

GeneView via analysis of contig annotation: RAI14 retinoic acid induced 14

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_006576->NM_015577

function

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


reference	NT_006576->NM_015577->NP_056392	34733993	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs162913 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_922596.1	353549	34643035	plus	C	alt_assembly_1	Celera	Celera	view	581
5	NW_001838932.2	947548	34709742	minus	G	alt_assembly_8	HuRef	HuRef	view	581
5	NT_006576.15	34733993	34796993	plus	C	ref_assembly	reference	reference	view	581

NCBI Resource Links

Submitter-Referenced
GenBank
NT_006576 AC008690 AC025769 AC055815 AC055815.3

dbSNP Blast Analysis

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

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .