Reference SNP(refSNP) Cluster Report: rs542977

Reference SNP(refSNP) Cluster Report: rs542977

refSNP ID: rs542977
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	83/129
Map to Genome Build:	36.3

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

HGVS Names
NM_152481.1:c.722+43G>T
NT_011109.15:g.7987037C>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss713747 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs542977 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
ss713747	SC_JCM\|AC024682.3_163975	fwd/B	G/T	ctgcctctggcccctacccagattcttccg	tcaggggatccttcctggtaatatgtgcag	07/27/00	04/07/04	83	Genomic	unknown
ss4932267	YUSUKE\|IMS-JST097769	rev/T	A/C	ctgcacatattaccaggaaggatcccctga	cggaagaatctgggtaggggccagaggcag	08/01/02	10/10/03	108	Genomic	unknown
ss12472802	WI_SSAHASNP\|chr19.NT_011109.15_7987037	rev/T	A/C	ctgcacatattaccaggaaggatcccctga	cggaagaatctgggtaggggccagaggcag	07/04/03	10/10/03	116	Genomic	unknown
ss75125900	ILLUMINA\|ILMN_Human_1M_rs542977	fwd/B	G/T	ctgcctctggcccctacccagattcttccg	tcaggggatccttcctggtaatatgtgcag	08/28/07	08/29/07	129	Genomic	unknown
ss81520982	HGSV\|Cor18555_SNV_20070510.chr19_40410659	rev/T	A/C	ctgcacatattaccaggaaggatcccctga	cggaagaatctgggtaggggccagaggcag	11/27/07	11/30/07	130	Genomic	unknown
ss81960468	HGSV\|Cor18956_SNV_20070510.chr19_40410659	rev/T	A/C	ctgcacatattaccaggaaggatcccctga	cggaagaatctgggtaggggccagaggcag	11/30/07	12/01/07	130	Genomic	unknown

Fasta sequence (Legend)

 TCTAGCCGCT TGCGGCCTGA GCTGCAGGTG GAAGCCTGCC ACGTCCAGTG CACCAATAAC
 ACACAGTTAA GGGTGGATTA CATCATTTTT GACAACTTCA GGCTCGATGA GAAGACAGAA
 TTTGTGTGGC TCGACTGTCC CTTAGGATCC ATGTACAGGT GATGGAATCC CTGCCTCTGG
 CCCCTACCCA GATTCTTCCG
 K
 TCAGGGGATC CTTCCTGGTA ATATGTGCAG AGGGATGAGT GGGCGTTCTT TGCAGTTCAG
 CCACGTAGTG GTCATCAGGA CAGTGCCAGG CCCTGCTCTT AAACAGTCCG AGGGGGACAC
 AGCCCAGGGT GGTGCGAGCC GGGATGGAAG AAGCCCAGGC AGACAGATGG GGCTGTGATG
 GGGGAAGCCC AGGAAGCTTA

GeneView

GeneView via analysis of contig annotation: TMEM162 transmembrane protein 162

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_011109->NM_152481

function

HuRef

NW_001838494->NM_152481

function

Celera

NW_927206->NM_152481

function

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


reference	NT_011109->NM_152481->NP_689694	7987037	reverse	intron

HuRef	NW_001838494->NM_152481->NP_689694	839384	reverse	intron

Celera	NW_927206->NM_152481->NP_689694	8003836	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs542977 maps exactly once on NCBI human chromosome 19

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
19	NW_001838494.1	839384	32227327	minus	C	alt_assembly_8	HuRef	HuRef	view	200
19	NW_927206.1	8003836	32432268	minus	C	alt_assembly_1	Celera	Celera	view	200
19	NT_011109.15	7987037	40410659	minus	C	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011294.1 AC002128

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC002128.1 NC_000019.8	AC024682.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss4932267	JBIC-allele		1478	AF					0.881	0.119

ss713747	CEPH		91	AF					0.828	0.172

	HapMap-CEU	European	120	IG	0.783	0.217		0.371	0.892	0.108

	HapMap-HCB	Asian	90	IG	0.667	0.267	0.067	0.273	0.800	0.200

	HapMap-JPT	Asian	88	IG	0.727	0.273		0.294	0.864	0.136

	HapMap-YRI	Sub-Saharan African	118	IG	0.627	0.288	0.085	0.200	0.771	0.229

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.280+/-0.248	270	210	0	0

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .