Reference SNP(refSNP) Cluster Report: rs1558241

Reference SNP(refSNP) Cluster Report: rs1558241

refSNP ID: rs1558241
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	88/129
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_207387.1:c.106-12739A>G
NT_010718.15:g.15975788T>C

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss14282948 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1558241 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
ss2401677	TSC-CSHL\|TSC0445924	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	10/20/00	04/07/04	88	Genomic	95 %
ss14282948	BCM_SSAHASNP\|chr17.NT_010718.14_15219445	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	11/05/03	10/25/06	119	Genomic	unknown
ss24595370	PERLEGEN\|afd0816008	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	08/10/04	09/13/04	123	Genomic	unknown
ss44031912	ABI\|hCV7460802	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	07/18/05	07/18/05	126	Genomic	unknown
ss66640353	ILLUMINA\|HumanHap300v1.1_rs1558241	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	11/09/06	11/09/06	127	Genomic	unknown
ss67133583	ILLUMINA\|HumanHap550v1.1_rs1558241	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	11/14/06	11/14/06	127	Genomic	unknown
ss67473453	ILLUMINA\|HumanHap650Yv1.0_rs1558241	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	11/14/06	11/14/06	127	Genomic	unknown
ss69193238	PERLEGEN\|PGP00816008	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	01/30/07	08/14/07	127	Genomic	unknown
ss70443322	ILLUMINA\|HumanHap300v2.0_rs1558241	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	04/18/07	11/18/07	127	Genomic	unknown
ss70632741	ILLUMINA\|HumanHap550v3.0__rs1558241	rev/T	A/G	ctctgagaaatgggctgttcctatgaagac	ctcctgcttggaactcaggttgttagggag	04/20/07	03/30/08	130	Genomic	unknown
ss71182923	ILLUMINA\|HumanHap650Yv3.0_rs1558241	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	04/23/07	04/23/07	127	Genomic	unknown
ss75552712	ILLUMINA\|ILMN_Human_1M_rs1558241	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	08/28/07	08/29/07	129	Genomic	unknown
ss76797264	AFFY\|AFFY_6_1M_SNP_A-8658670	rev/T	A/G	ctgttcctatgaagac	ctcctgcttggaactc	08/28/07	08/30/07	130	Genomic	unknown
ss83835276	KRIBB_YJKIM\|KHS554029	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	12/04/07	12/05/07	130	Genomic	unknown
ss85555833	HGSV\|Cor18517_SNV_20070510.chr17_16319164	fwd/B	C/T	ctccctaacaacctgagttccaagcaggag	gtcttcataggaacagcccatttctcagag	12/06/07	12/09/07	130	Genomic	unknown

Fasta sequence (Legend)

 ATACCTTCTG GCAAATGCAT TCAAGTCCAT TTGTCCCTCT CTGCAGTACA TTCTGCCCAA
 GTGAAATGAA ACATTTGGTT CATCCTGAgg ccgggcgcgg tggctcacgc ctgtaatcct
 agcactttgg gaggccgagg caggtggatc acgaggtcag gagatgagac catcctggct
 aacatggtga aaccccgtct ctattgaaag tacaaaaaat tagccgggcg tggtggtggg
 cgcctgtagt cccagctact cgggaggctg aggcaggaga atggcgtgaa cccaggaggc
 ggagcttgca gtgagccaag attgtgccac cgctgcactc cagcctgggc aacggtgcaa
 gactccgtct caaaaaaaaa aaaaaaagag agaaaCATTT GGTTCATCCT CAAAGGATTT
 TCAGGTAAAA TGGCAAAGAG GTAGAGGAAC GACTTAGAGG ATCCTTCTGG CTCCCTAACA
 ACCTGAGTTC CAAGCAGGAG
 Y
 GTCTTCATAG GAACAGCCCA TTTCTCAGAG TGAAAAGCTG GGGGCTGGAA GGTTGTCTCA
 TACAGTGAGC TAGTGGCAGG GATGGGGCGC TCCAGAGCCC CTAGAAATTT CTGACTCTGC
 CTCTATGAGC CCTTGGAAGT TAAgtattag ccagggttct ctcgagacac agaactgata
 agatgtgtgt gtgtgtggag agagaggaag gaattgattt attttaagga attggctcac
 atgattgtgg gggctggcga gtctgaaatc tgcagggcag gctgggaagc tggggaccca
 ggaaggagct ggcagtgctg tctggagtct gaaggcagaa tttcttcttc ctcagggacc
 tctcttttct cttggagcct tcaactgatt gaatgaggct cacccatatt atggaaagta
 atcagctttT ATCCATTTAT GCttttgaga cagagtctct ctgtcaccca ggctacagtg
 tggtggtgtg atcctagctc

GeneView

GeneView via analysis of contig annotation: C17orf76 chromosome 17 open reading frame 76

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_010718->NM_207387

function

HuRef

NW_001838406->NM_207387

function

Celera

NW_926606->NM_207387

function

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


reference	NT_010718->NM_207387->NP_997270	15975788	reverse	intron

HuRef	NW_001838406->NM_207387->NP_997270	231095	forward	intron

Celera	NW_926606->NM_207387->NP_997270	693631	reverse	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs1558241 maps exactly once on NCBI human chromosome 17

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
17	NW_001838406.2	231095	16244877	minus	A	alt_assembly_8	HuRef	HuRef	view	500
17	NW_926606.1	693631	16281350	plus	T	alt_assembly_1	Celera	Celera	view	500
17	NT_010718.15	15975788	16319164	plus	T	ref_assembly	reference	reference	view	500

NCBI Resource Links

Submitter-Referenced
GenBank
NT_010718

dbSNP Blast Analysis
GenBank HTGS Finished:	GenBank HTGS Draft:
AC005822.1 AC127540.10 AJ009612.5 NC_000017.9	AC126385.3

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss14282948	HapMap-CEU	European	120	IG	0.183	0.500	0.317	1.000	0.433		0.567

	HapMap-HCB	Asian	90	IG	0.778	0.222		0.403	0.889		0.111

	HapMap-JPT	Asian	90	IG	0.711	0.244	0.044	0.479	0.833		0.167

	HapMap-YRI	Sub-Saharan African	120	IG	0.800	0.150	0.050		0.875		0.125

	CHMJ	Asian	74	IG					0.838	0.027	0.135

ss2401677	WICGR8_asian_pooled		84	AF					0.890		0.110

	WICGR6_caucasian_pooled		96	AF					0.370		0.630

ss24595370	AFD_EUR_PANEL	European	48	IG	0.167	0.542	0.292	0.655	0.438		0.562

	AFD_AFR_PANEL	African American	46	IG	0.652	0.261	0.087	0.273	0.783		0.217

	AFD_CHN_PANEL	Asian	48	IG	0.708	0.292		0.439	0.854		0.146

ss69193238	HapMap-CEU	European	120	GF	0.183	0.500	0.317		0.433		0.567

	HapMap-HCB	Asian	90	GF	0.778	0.222			0.889		0.111

	HapMap-JPT	Asian	90	GF	0.711	0.244	0.044		0.833		0.167

	HapMap-YRI	Sub-Saharan African	118	GF	0.780	0.169	0.051		0.864		0.136

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss14282948	269	157	77	35
ss24595370	71	36	26	9
ss69193238	269	156	77	35

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs1558241	332	191	98	42

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5144	ss14282948	C/C	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	r23_ch17_YRI_illumina:infinium_genotyping_2.0.0
5144	ss69193238	C/T	CSHL-HAPMAP	HapMap-YRI	NA19192	YOR112.03	chr17-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

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .