Reference SNP(refSNP) Cluster Report: rs155245

Reference SNP(refSNP) Cluster Report: rs155245

refSNP ID: rs155245
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:	C/T
Ancestral Allele:	C
Clinical Association:	unknown

HGVS Names
NM_006711.2:c.677-1505A>G
NM_080594.1:c.677-1505A>G
NT_037887.4:g.2247233T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1617458 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs155245 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
ss292861	KWOK\|OVLP-000621-280559	fwd/B	C/T	cctcaagaattgtctggtagctggggatac	gggagcccaagcgcagccccttctgtgccc	06/30/00	10/10/03	79	Genomic	97 %
ss342968	KWOK\|OVLP-000621-94397	fwd/B	C/T	cctcaagaattgtctggtagctggggatac	gggagcccaagcgcagccccttctgtgccc	06/30/00	10/10/03	79	Genomic	99 %
ss402680	KWOK\|OVLP-000621-250470	fwd/B	C/T	cctcaagaattgtctggtagctggggatac	gggagcccaagcgcagccccttctgtgccc	06/30/00	10/10/03	85	Genomic	99 %
ss413173	KWOK\|OVLP-000621-277598	fwd/B	C/T	cctcaagaattgtctggtagctggggatac	gggagcccaagcgcagccccttctgtgccc	06/30/00	10/10/03	85	Genomic	99 %
ss1144016	KWOK\|OVLP-000804-425384	rev/T	A/G	gggcacagaaggggctgcgcttgggctccc	gtatccccagctaccagacaattcttgagg	09/02/00	10/10/03	86	Genomic	99 %
ss1145420	KWOK\|OVLP-000804-433228	rev/T	A/G	gggcacagaaggggctgcgcttgggctccc	gtatccccagctaccagacaattcttgagg	09/02/00	10/10/03	86	Genomic	99 %
ss1238705	KWOK\|OVLP-000804-417920	rev/T	A/G	gggcacagaaggggctgcgcttgggctccc	gtatccccagctaccagacaattcttgagg	09/02/00	10/10/03	86	Genomic	97 %
ss1238981	KWOK\|OVLP-000804-420808	rev/T	A/G	gggcacagaaggggctgcgcttgggctccc	gtatccccagctaccagacaattcttgagg	09/02/00	10/10/03	86	Genomic	97 %
ss1617458	KWOK\|OVLP-000925-522670	rev/T	A/G	gggcacagaaggggctgcgcttgggctccc	gtatccccagctaccagacaattcttgagg	10/04/00	05/16/04	87	Genomic	99 %
ss1645459	KWOK\|OVLP-000925-513748	rev/T	A/G	gggcacagaaggggctgcgcttgggctccc	gtatccccagctaccagacaattcttgagg	10/04/00	10/10/03	87	Genomic	97 %
ss1646055	KWOK\|OVLP-000925-525042	rev/T	A/G	gggcacagaaggggctgcgcttgggctccc	gtatccccagctaccagacaattcttgagg	10/04/00	10/10/03	87	Genomic	97 %
ss2515551	SC_JCM\|AC024088.4_68442	fwd/B	C/T	cctcaagaattgtctggtagctggggatac	gggagcccaagcgcagccccttctgtgccc	11/03/00	10/10/03	89	Genomic	unknown
ss6606122	WI_SSAHASNP\|NT_010552.11_815736	fwd/B	C/T	cctcaagaattgtctggtagctggggatac	gggagcccaagcgcagccccttctgtgccc	02/12/03	10/10/03	111	Genomic	unknown
ss75223728	ILLUMINA\|ILMN_Human_1M_rs155245	fwd/B	C/T	cctcaagaattgtctggtagctggggatac	gggagcccaagcgcagccccttctgtgccc	08/28/07	08/29/07	129	Genomic	unknown

Fasta sequence (Legend)

 TTGTGTTTGG AAACAAGCAG TCTCAGAGAG GTGGCTCTGC ATGTAGATGG CACTGAAACA
 CACGCCATGT GCATGAAGCG AGGAGAGGCA GTGTGGGATG TGGGCTCCAG GGAGAGAGGA
 AAGGAAATAG AGGTGCAAAC CCAGGAACCC CAGGGGAGCA TGCACCCCGA CCTCAAGAAT
 TGTCTGGTAG CTGGGGATAC
 Y
 GGGAGCCCAA GCGCAGCCCC TTCTGTGCCC TAAGGGGTAA AGGGCTCTTT TGTTTTCTCA
 ACTACCTTTA AGGCACATGG GGACTAACTC CGGCATGTGG CTATGTATTC AGAACATACT
 TAAGAGGTTT AACTTCAGTA AACTCAGCCT AAGTTAGCCC AAATTAGGGA TTTCACAGCA
 CTGACTCTAT AATAATGAAG

GeneView

GeneView via analysis of contig annotation: RNPS1 RNA binding protein S1, serine-rich domain

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_037887->NM_006711

function

reference

NT_037887->NM_080594

function

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


reference	NT_037887->NM_006711->NP_006702	2247233	reverse	intron

reference	NT_037887->NM_080594->NP_542161	2247233	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs155245 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_001838339.2	390740	2233277	minus	A	alt_assembly_8	HuRef	HuRef	view	200
16	NT_037887.4	2247233	2247233	plus	T	ref_assembly	reference	reference	view	200
16	NW_926018.1	2237310	2521660	plus	T	alt_assembly_1	Celera	Celera	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
AC024088 AC005212 AC007162 AC012171 AC024088.4

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss1617458	CEPH		184	AF					0.940	0.060

	HapMap-CEU	European	120	IG			1.000			1.000

	HapMap-HCB	Asian	90	IG			1.000			1.000

	HapMap-JPT	Asian	90	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	112	IG	0.071	0.589	0.339	0.050	0.366	0.634

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.179+/-0.240	270	210	0	0

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 .