Reference SNP(refSNP) Cluster Report: rs678560

Reference SNP(refSNP) Cluster Report: rs678560

refSNP ID: rs678560
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:	C/T
Ancestral Allele:	Not available
Clinical Association:	unknown

HGVS Names
NM_017947.2:c.1072G>A
NP_060417.2:p.V358M
NT_010966.13:g.15274194G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss10915897 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs678560 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
ss852096	SC_JCM\|AP001155.2_75058	fwd/B	C/T	cattggggtactggagagaggacagggcca	gtaggtatactgagccaaggtgaaggtgtg	07/27/00	10/10/03	83	Genomic	unknown
ss10915897	BCM_SSAHASNP\|chr18.NT_010966.13_15274195	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	06/30/03	10/25/06	116	Genomic	unknown
ss13515753	SC_JCM\|chr18.NT_010966.13_15274195	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	10/31/03	11/07/03	123	Genomic	unknown
ss21502907	SSAHASNP\|WGSA-200403-chr18.chr18.NT_010966.13_15274195	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	03/20/04	03/20/04	123	Genomic	unknown
ss23751479	PERLEGEN\|afd1798656	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	08/10/04	09/13/04	123	Genomic	unknown
ss24796557	SEQUENOM\|sqnm141354	fwd/B	C/T	cattggggtactggagagaggacagggcca	gtaggtatactgagccaaggtgaaggtgtg	06/18/04	08/05/04	123	cDNA	unknown
ss28505153	MGC_GENOME_DIFF\|BC012079x29823167-G15274195A	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	08/25/04	08/25/04	126	cDNA	unknown
ss44120246	ABI\|hCV549404	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	07/18/05	07/18/05	126	Genomic	unknown
ss48420388	APPLERA_GI\|hCV549404	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	09/28/05	11/03/06	126	Genomic	unknown
ss67860035	ILLUMINA\|HumanHap650Yv1.0_rs678560	fwd/B	C/T	cattggggtactggagagaggacagggcca	gtaggtatactgagccaaggtgaaggtgtg	11/14/06	11/14/06	127	Genomic	unknown
ss69211359	PERLEGEN\|PGP01798656	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	01/30/07	08/14/07	127	Genomic	unknown
ss71478813	ILLUMINA\|HumanHap650Yv3.0_rs678560	fwd/B	C/T	cattggggtactggagagaggacagggcca	gtaggtatactgagccaaggtgaaggtgtg	04/23/07	04/23/07	127	Genomic	unknown
ss74812798	AFFY\|SNP_M-288325	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	08/09/07	08/09/07	128	Genomic	unknown
ss74816219	AFFY\|SNP_M-312261	fwd/B	C/T	cattggggtactggagagaggacagggcca	gtaggtatactgagccaaggtgaaggtgtg	08/09/07	08/09/07	128	Genomic	unknown
ss75347016	ILLUMINA\|ILMN_Human_1M_rs678560	fwd/B	C/T	cattggggtactggagagaggacagggcca	gtaggtatactgagccaaggtgaaggtgtg	08/28/07	08/29/07	129	Genomic	unknown
ss76594945	AFFY\|AFFY_6_1M_SNP_A-8456223	fwd/B	C/T	agagaggacagggcca	gtaggtatactgagcc	08/28/07	08/30/07	129	Genomic	unknown
ss82556043	HGSV\|Cor19240_SNV_20070510.chr18_32039091	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	11/30/07	12/03/07	130	Genomic	unknown
ss90761275	BCMHGSC_JDW\|JWB-1087565	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	02/26/08	02/29/08	129	Genomic	unknown
ss110364111	1000GENOMES\|CEU.trio.12.15.2008_3493699_chr18_32039091	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	12/15/08	12/17/08	130	Genomic	unknown
ss114254800	1000GENOMES\|NA19240_2008_12_16_3148650_chr18_32039091	rev/T	A/G	cacaccttcaccttggctcagtatacctac	tggccctgtcctctctccagtaccccaatg	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 GTCTGGAACT AGGATGAGTT GTAATAAAGT CAGCAGGATG GAAAGAAAAC CCACCTGGGA
 GTAACCAATG ATGTTCCCTT TGTCATCCAG CACATTAAAA TTGATGATTG GGCCCTGAAC
 CTCAGGGCTG CTGAACTCAG AATCGCTGTA AATCCGCACC ACAGGGGCTC CATTGGGGTA
 CTGGAGAGAG GACAGGGCCA
 Y
 GTAGGTATAC TGAGCCAAGG TGAAGGTGTG CTGCTTTATA TTCTCCATTC CACCTCAAAT
 CAATCATGAA ACACAAGAGA ATCATGAGCT TTATGTAAAT TCTCAATTCA CTCTTTTTTT
 TTTTTTTTTT TTTGAGACAC GGTCTCACTC ACTCTGTCAC CCAGGCTGGA GTGCAGTGGT
 ATGATCACAG CTCACTGCAG CCTCAACCTC CTGGGCTCAG GTGATCCTCT CACCTCAGCC
 TCCCAAGTAG CTGGGACGAC AGGCATTCAC CACCATGCCT GACTAATTTT TGTATTTTTT
 GCAGAGATGG AGTTTCACCA TGTTGCCCAG GCTTGTCTTG AGCTCCTGGG CTCAAGTAAT
 CCACCTGCCT CAGCCTCCCA AAGTGCTGGG ATTACAGGCA TGAGCCACCA CGCCTGGCAC
 CACTAACTCA CTTTTAAGAA AACAAGTTTG TTATAACTGG CAAACCTGGA CCTCACATTA
 ATAATTTTAA ATGTGTGTAA

GeneView

GeneView via analysis of contig annotation: MOCOS molybdenum cofactor sulfurase

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_010966->NM_017947

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	mRNA pos	Function	dbSNP allele	Protein residue	Codon pos	Amino acid pos


reference	NT_010966->NM_017947->NP_060417	15274195	forward	1095	missense	A	Met [M]	1	358
					contig reference	G	Val [V]	1	358

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs678560 maps exactly once on NCBI human chromosome 18

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
18	NW_927095.1	15261420	30593015	minus	A	alt_assembly_1	Celera	Celera	view	200
18	NW_001838467.2	10756782	30644020	plus	T	alt_assembly_8	HuRef	HuRef	view	200
18	NT_010966.13	15274195	32039091	minus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
dbSTS	GenBank
sqnm141354	NT_010966 AP001158 BC012079

dbSNP Blast Analysis
NCBI RefSeq NM (mRNA):	GenBank HTGS Draft:
NM_017947.2	AP001155.2 AP001158.3

UniGene Cluster ID
405028

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss10915897	HapMap-CEU	European	120	IG		0.067	0.933	1.000	0.033	0.967

	HapMap-HCB	Asian	88	IG	0.023	0.136	0.841	0.251	0.091	0.909

	HapMap-JPT	Asian	84	IG	0.024	0.190	0.786	0.584	0.119	0.881

	HapMap-YRI	Sub-Saharan African	110	IG	0.018	0.364	0.618	0.317	0.200	0.800

ss23751479	AFD_EUR_PANEL	European	48	IG			1.000			1.000

	AFD_AFR_PANEL	African American	46	IG		0.435	0.565	0.200	0.217	0.783

	AFD_CHN_PANEL	Asian	48	IG		0.167	0.833	0.752	0.083	0.917

ss24796557	CEPH		184	AF					0.080	0.920

ss48420388	AGI_ASP population	multiple	70	IG		0.143	0.857	0.655	0.071	0.929

ss69211359	HapMap-CEU	European	120	GF		0.067	0.933		0.033	0.967

	HapMap-HCB	Asian	90	GF	0.022	0.156	0.822		0.100	0.900

	HapMap-JPT	Asian	90	GF	0.022	0.244	0.733		0.144	0.856

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.433	0.550		0.233	0.767

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss10915897	269
ss23751479	71
ss48420388	38
ss69211359	269

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs678560	370

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5288	ss10915897	A/A	CSHL-HAPMAP	HapMap-YRI	NA19210	YOR050.03	r23_ch18_YRI_perlegen:genotyping_1.0.0	5531165
5288	ss69211359	A/G	CSHL-HAPMAP	HapMap-YRI	NA19210	YOR050.03	chr18-HapMap-YRI

Genotype data submitted for	379	samples from	370	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
	UNKNOWN	UNKNOWN	UNKNOWN

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Revised: May 25, 2006 1:38 PM .