Reference SNP(refSNP) Cluster Report: rs360727

Reference SNP(refSNP) Cluster Report: rs360727

refSNP ID: rs360727
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/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_001562.2:c.*230A>G
NT_033899.7:g.15576505T>C

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss2018959 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs360727 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
ss457373	KWOK\|OVLP-000621-393176	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	06/30/00	10/10/03	79	Genomic	99 %
ss680567	SC_JCM\|AP002502.1_38312	fwd/T	A/G	aggcaggagaatcacttgcactccggaggt	gaggttgtggtgagccgagattgcaccatt	07/27/00	10/10/03	83	Genomic	unknown
ss1526488	LEE\|442621	fwd/T	A/G	aggcaggagaatcacttgcactccggaggt	gaggttgtggtgagccgagattgcaccatt	09/13/00	10/10/03	126	cDNA	unknown
ss2018959	KWOK\|OVLP-000925-554892	fwd/T	A/G	aggcaggagaatcacttgcactccggaggt	gaggttgtggtgagccgagattgcaccatt	10/06/00	10/10/03	87	Genomic	99 %
ss5565052	TSC-CSHL\|TSC0640206	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	09/21/02	10/10/03	110	Genomic	unknown
ss6828149	WI_SSAHASNP\|NT_033899.3_1552484	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	02/12/03	10/10/03	111	Genomic	unknown
ss7988463	IIPGA-WEISS-MARTINEZ\|IIPGA-IL18_23211	fwd/T	A/G	aggcaggagaatcacttgcactccggaggt	gaggttgtggtgagccgagattgcaccatt	04/11/03	04/07/04	126	Genomic	unknown
ss10668649	BCM_SSAHASNP\|chr11.NT_033899.5_15557756	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	06/29/03	10/10/03	116	Genomic	unknown
ss12140015	WI_SSAHASNP\|chr11.NT_033899.5_15557756	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	07/04/03	10/10/03	116	Genomic	unknown
ss15803875	SC_SNP\|NT_033899.6_15557873	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	11/17/03	11/22/03	120	Genomic	unknown
ss20812980	SSAHASNP\|WGSA-200403-chr11.chr11.NT_033899.6_15557873	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	03/19/04	03/19/04	121	Genomic	unknown
ss40028249	ABI\|hCV27137506	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	07/16/05	07/16/05	126	Genomic	unknown
ss76869432	CGM_KYOTO\|11896	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	09/12/07	09/12/07	129	cDNA	unknown
ss88794813	BCMHGSC_JDW\|JWB-0481539	rev/B	C/T	aatggtgcaatctcggctcaccacaacctc	acctccggagtgcaagtgattctcctgcct	02/26/08	02/28/08	129	Genomic	unknown

Fasta sequence (Legend)

 GTGACATCAT ATTCTTTCAG AGAAGTGTCC CAGGACATGA TAATAAGATG CAATTTGAAT
 CTTCATCATA CGAAGGATAC TTTCTAGCTT GTGAAAAAGA GAGAGACCTT TTTAAACTCA
 TTTTGAAAAA AGAGGATGAA TTGGGGGATA GATCTATAAT GTTCACTGTT CAAAACGAAG
 ACTAGCTATT AAAATTTCAT gccgggcgca gtggctcacg cctgtaatcc cagccctttg
 ggaggctgag gcgggcagat caccagaggt caggtgttca agaccagcct gaccaacatg
 gtgaaacctc atctctacta aaaatacaaa aaattagctg agtgtagtga cccatgccct
 caatcccagc tactcaagag gctgaggcag gagaatcact tgcactccgg aggt
 R
 gaggttgtgg tgagccgaga ttgcaccatt gcgctctagc ctgggcaaca acagcaaaac
 tccatctcaa aaaataaaat aaataaataa acaaataaaA AATTCATAAT GTGAACTGTC
 TGAATTTTTA TGTTTAGAAA GATTATGAGA TTATTAGTCT ATAATTGTAA TGGTGAAATA
 AAATAAATAC TAGTCTTGAA AAACATCATT AAGAAATGAA TGAACTTTCA CAAAAGCAAA
 CAAACAGACT TTCCCTTATT TAAGTGaata aaataaaata aaataaaata aTGTTTAAAA
 AATTCATAGT TTGAAAACAT TCTACATTGT TAATTGGCat attaattata cttaatataa
 ttatttttaa atCTTTTGGG TTATTAGTCC TAATGACAAA AGATATTGAT ATTTGAACTT
 TCTAATTTTT AAGAATATCG TTAAACCATC AATATTTTTA TAAGGAGGCC AC

GeneView

GeneView via analysis of contig annotation: IL18 interleukin 18 (interferon-gamma-inducing factor)

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_033899->NM_001562

function

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


reference	NT_033899->NM_001562->	15576505	reverse	1032	3' UTR

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs360727 maps exactly once on NCBI human chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NW_001838042.2	8748799	107938210	plus	G	alt_assembly_8	HuRef	HuRef	view	414
11	NW_925173.1	22036227	109167327	minus	C	alt_assembly_1	Celera	Celera	view	414
11	NT_033899.7	15576505	111519299	minus	T	ref_assembly	reference	reference	view	414

NCBI Resource Links

Submitter-Referenced
GenBank
NT_033899.7 AC009648 AC010815.6 AP002007 Hs.83077

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Finished:	GenBank HTGS Draft:
NM_001562.2	AP002007.4	AP002502.1

UniGene Cluster ID
83077

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss7988463	D-0	African American	46	IG	0.043	0.217	0.739	0.479	0.152	0.848

	E-0	European	40	IG			1.000			1.000

	E-1	European	6	IG		0.333	0.667		0.167	0.833

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.159+/-0.233	47	26	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: NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .