Reference SNP(refSNP) Cluster Report: rs1224499

Reference SNP(refSNP) Cluster Report: rs1224499

refSNP ID: rs1224499
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	87/129
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_152734.3:c.424+3577T>G
NT_007592.14:g.27732037T>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss44770107 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1224499 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
ss1800367	KWOK\|OVLP-000925-635688	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	10/05/00	10/10/03	87	Genomic	99 %
ss2586599	SC_JCM\|AL122034.11_28581	rev/T	A/C	ttaagttggccagaaaatgaccaaagtaaa	aaaataattggctgaacatgctagcgcctg	11/03/00	10/10/03	89	Genomic	unknown
ss13099516	SC_SNP\|NT_007592.13_27670914	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	10/22/03	10/31/03	119	Genomic	unknown
ss17116164	CSHL-HAPMAP\|CSHL-HuAA-200402.chr6.NT_007592.13_27670914	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	02/17/04	10/26/06	120	Genomic	unknown
ss19666874	CSHL-HAPMAP\|CSHL-HuDD-200402.chr6.NT_007592.13_27670914	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	02/20/04	03/04/04	120	Genomic	unknown
ss22473172	SSAHASNP\|WGSA-200403-chr6.chr6.NT_007592.13_27670914	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	03/21/04	03/21/04	121	Genomic	unknown
ss24313990	PERLEGEN\|afd4063700	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	08/10/04	09/13/04	123	Genomic	unknown
ss44770107	ABI\|hCV11396905	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	07/19/05	11/03/06	126	Genomic	unknown
ss66357883	AFFY\|SNP_A-1985692	rev/T	A/C	aaatgaccaaagtaaa	aaaataattggctgaa	10/29/06	08/14/07	127	Genomic	unknown
ss68973678	PERLEGEN\|PGP04063700	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	01/30/07	08/14/07	127	Genomic	unknown
ss76074509	AFFY\|AFFY_6_1M_SNP_A-1985692	rev/T	A/C	aaatgaccaaagtaaa	aaaataattggctgaa	08/28/07	08/29/07	129	Genomic	unknown
ss78358063	HGSV\|Cor12878_SNV_20070510.chr6_36981765	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	10/17/07	10/19/07	129	Genomic	unknown
ss83700252	HGSV\|Cor19240_SNV_20070510.chr6_36981765	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	11/30/07	12/05/07	130	Genomic	unknown
ss85402836	HGSV\|Cor19129_SNV_20070510.chr6_36981765	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	12/06/07	12/09/07	130	Genomic	unknown
ss93443388	BCMHGSC_JDW\|JWB-2126136	fwd/B	G/T	caggcgctagcatgttcagccaattatttt	tttactttggtcattttctggccaacttaa	02/26/08	03/04/08	129	Genomic	unknown

Fasta sequence (Legend)

 TTTATAGTCA CTTTACTCCT GCCGGCCATC CCCTTGGTTT TTACCATTTC CATGGAATCA
 TTGAGTCTTA AAGCCAGAAA AGAATTTTAG AGTTAATCTA GTACATACCC CATTTTATAA
 AAGAGGTAAC TGAGGCCAGG AGAGGTAAAG GAGCTTGCTT ACCCAGCTAA AAGTGGCAAA
 ATCACACTTG AACCCTAGTT TCTTAACTCC CTCTAGCATT CTGTCCAAGA TATCACACTT
 ACAGCCTGCC ATCTCTGCCC TCAGTCAAGC CAGGCGCTAG CATGTTCAGC CAATTATTTT
 K
 TTTACTTTGG TCATTTTCTG GCCAACTTAA AAATAACATA TTCATTTCTA CTGAGGAAGC
 CTGGGATAGT TCTCACATAC AGTGAAAAGG CACACATTTG GAACTCGATG CATCCCGTAA
 CCTTCAAAGG AAGGATGAAG TAGATCCAGC AACATCAAGA AGTTTTGGAA ATAGCAAATC
 ATTTATTGGC CTCAAACTAA GAATCTAGTA AGACTTAGAG AGTCCAGATC TGTGCTCAAA
 GATGAACTGC TTAGACCGCA AGGAAAACCT TCCTCTTTTA TTTGCAAAAT AAGCTTACCT

GeneView

GeneView via analysis of contig annotation: C6orf89 chromosome 6 open reading frame 89

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_007592->NM_152734

function

HuRef

NW_001838980->NM_152734

function

Celera

NW_923073->NM_152734

function

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


reference	NT_007592->NM_152734->NP_689947	27732037	forward	intron

HuRef	NW_001838980->NM_152734->NP_689947	9864384	forward	intron

Celera	NW_923073->NM_152734->NP_689947	9893151	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1224499 maps exactly once on NCBI human chromosome 6

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
6	NW_001838980.1	9864384	36592075	plus	G	alt_assembly_8	HuRef	HuRef	view	300
6	NT_007592.14	27732037	36981765	plus	T	ref_assembly	reference	reference	view	300
6	NW_923073.1	9893151	38428830	plus	G	alt_assembly_1	Celera	Celera	view	300

NCBI Resource Links

Submitter-Referenced
GenBank
NT_007592 AC073394 AL122034.11

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AL122034.29 NC_000006.10	AC073394.2

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	T
ss17116164	CHMJ	Asian	74	IG					0.824	0.176

ss24313990	AFD_EUR_PANEL	European	46	IG	0.609	0.348	0.043	1.000	0.783	0.217

	AFD_AFR_PANEL	African American	46	IG	0.913	0.087		1.000	0.957	0.043

	AFD_CHN_PANEL	Asian	48	IG	0.792	0.208		0.584	0.896	0.104

ss44770107	HapMap-CEU	European	116	IG	0.603	0.293	0.103	0.100	0.750	0.250

	HapMap-HCB	Asian	90	IG	0.800	0.156	0.044	0.100	0.878	0.122

	HapMap-JPT	Asian	88	IG	0.727	0.250	0.023	1.000	0.852	0.148

	HapMap-YRI	Sub-Saharan African	120	IG	1.000				1.000

ss66357883	HapMap-CEU	European	118	GF	0.610	0.288	0.102		0.754	0.246

	HapMap-HCB	Asian	90	GF	0.800	0.156	0.044		0.878	0.122

	HapMap-JPT	Asian	90	GF	0.733	0.244	0.022		0.856	0.144

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

ss68973678	HapMap-CEU	European	118	GF	0.593	0.305	0.102		0.746	0.254

	HapMap-HCB	Asian	90	GF	0.800	0.156	0.044		0.878	0.122

	HapMap-JPT	Asian	90	GF	0.711	0.267	0.022		0.844	0.156

	HapMap-YRI	Sub-Saharan African	120	GF	1.000				1.000

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss24313990	71	54	15	1
ss44770107	268	206	48	10
ss66357883	267
ss68973678	268	208	49	10

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs1224499	332	257	61	11

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5211	ss44770107	G/G	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	r23_ch6_JPT_affymetrix:genechip500k	3250109
5211	ss66357883	C/C	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	chr6-HapMap-JPT
5211	ss68973678	G/T	CSHL-HAPMAP	HapMap-JPT	NA18972	JA18972	chr6-HapMap-JPT
5298	ss44770107	G/T	CSHL-HAPMAP	HapMap-YRI	NA19120	YOR060.01	r23_ch6_YRI_affymetrix:genechip500k	3250109
5298	ss66357883	C/C	CSHL-HAPMAP	HapMap-YRI	NA19120	YOR060.01	chr6-HapMap-YRI
5298	ss68973678	G/G	CSHL-HAPMAP	HapMap-YRI	NA19120	YOR060.01	chr6-HapMap-YRI

Genotype data submitted for	341	samples from	332	individuals	Individual with multiple genotypes submission:	270

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

UNKNOWN

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Revised: May 25, 2006 1:38 PM .