Reference SNP(refSNP) Cluster Report: rs6429757

Reference SNP(refSNP) Cluster Report: rs6429757

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	116/130
Map to Genome Build:	36.3

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

HGVS Names
NM_024758.3:c.313G>C
NP_079034.3:p.Gly105Arg
NT_004873.16:g.2302688C>G

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss9837663 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs6429757 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
ss9837663	BCM_SSAHASNP\|chr1.NT_004873.14_2287015	fwd/B	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	06/27/03	04/07/04	116	Genomic	unknown
ss11368634	WI_SSAHASNP\|chr1.NT_004873.14_2287015	fwd/B	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	07/03/03	10/10/03	116	Genomic	unknown
ss16407060	CSHL-HAPMAP\|CSHL-HuAA-200402.chr1.NT_004873.15_2287015	fwd/B	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	02/17/04	03/04/04	120	Genomic	unknown
ss19112765	CSHL-HAPMAP\|CSHL-HuDD-200402.chr1.NT_004873.15_2287015	fwd/B	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	02/20/04	03/04/04	120	Genomic	unknown
ss19842408	CSHL-HAPMAP\|CSHL-HuFF-200402.chr1.NT_004873.15_2287015	fwd/B	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	02/21/04	03/04/04	120	Genomic	unknown
ss20460228	SSAHASNP\|WGSA-200403-chr1.chr1.NT_004873.15_2287015	fwd/B	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	03/18/04	03/18/04	121	Genomic	unknown
ss28510431	MGC_GENOME_DIFF\|BC005090x37549541-C2287015G	fwd/B	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	08/25/04	08/25/04	126	cDNA	unknown
ss43897858	ABI\|hCV2846010	fwd/	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	07/18/05	07/18/05	126	Genomic	unknown
ss66182792	AFFY\|SNP_A-2229373	fwd/B	C/G	ctaggattgactgtcc	aagcatcactgattct	10/27/06	03/31/08	127	Genomic	unknown
ss68759529	PERLEGEN\|PGP04755762	fwd/	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	01/30/07	03/31/08	127	Genomic	unknown
ss76249606	AFFY\|AFFY_6_1M_SNP_A-2229373	fwd/	C/G	ctaggattgactgtcc	aagcatcactgattct	08/28/07	08/30/07	130	Genomic	unknown
ss82226705	KRIBB_YJKIM\|KHS210602	fwd/	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	11/30/07	12/02/07	130	Genomic	unknown
ss87246568	BCMHGSC_JDW\|JWB-0014815	fwd/	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	02/26/08	02/26/08	129	Genomic	unknown
ss104802409	KRIBB_YJKIM\|KHS1108849	fwd/	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	06/09/08	06/09/08	130	Genomic	unknown
ss108014678	1000GENOMES\|CEU.trio.12.15.2008_19637_chr1_15782437	fwd/	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	12/15/08	12/15/08	130	Genomic	unknown
ss110100160	1000GENOMES\|NA19240_2008_12_16_19951_chr1_15782437	fwd/	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	12/16/08	12/17/08	130	Genomic	unknown
ss118519448	ILLUMINA-UK\|NA18507_000018827_NCBI36.1_chr1_15782437	fwd/	C/G	ggagggcccccgtgctaggattgactgtcc	aagcatcactgattcttcccggatgcggcg	01/21/09	01/21/09	130	Genomic	99 %

Fasta sequence (Legend)

 TGCAGGGAAC TACTCTGGCT CTTGCAGACT GACATTACCC AAGGTCAGAG GAATACAGCC
 AGCTGCTACA ATTTTCTCAT AGGCCTCTTG AATTCGCCGG CAGCTGTCCT GAAGGTTGTA
 AAGATTGACA TTCACATCGC CTAGGTCTGC AACCATGAGG GACTGGAAGG GGAGGGCCCC
 CGTGCTAGGA TTGACTGTCC
 S
 AAGCATCACT GATTCTTCCC GGATGCGGCG AGGTCCGAAT CTGCAGAAGG AAGAATCATC
 CTGTCAGCCA TCATCTGCAG AGATTTCAGG CTTTGCTTAG GCcagggctt ctcagcctca
 gcaatttggg gccagatgat tccgtgtcgc ggcattgcat aatggaatgc ttagcagcat
 cccggcctgt actcactagg tgccagtagc acccttcctc caaggtgtaa caacccaaaa
 cgcctccaga tactgccaaa tgtccccgga gtgcaaaacc gccccacttg agaatcaccg
 ATCTAGGCTA TGTATCGAAG AGACTAAATA AGTGTACTAA ATGGCATTAg tgaatttcat
 gatctacctg agtctcagtt tcctaatttg taaaatattt accttgcact gtagtaaaaa
 ttaaatgagg taatctatgc aaagcacctt gcacttagga gacatttaat aagtgctggc
 tttcatAATT CAGATCAGTA CGGTCAGATA TAGTGTTGCT GAGCTGAATC AGAAA

GeneView

GeneView via analysis of contig annotation:

View more variation on this gene (click to hide).

Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

Function	mRNA				Protein
Function	mRNA to Chr	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via analysis of contig annotation: N/A.

GeneView via direct blast against RefSeq sequences (used when no gene model is available):

Function	Chr	mRNA				Protein
Function	Chr	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A

Integrated Maps:

Genome Build	Chr	Chr Pos	Contig	Contig Pos	SNP to Chr	Contig allele	Group term	Group label	Contig label	Neighbor SNP	Map Method

doesn't map to any assembly.

NCBI Resource Links

Resource

Submitter-Referenced
GenBank
NT_004873 BC005090

dbSNP Blast Analysis

UniGene Cluster ID
461532

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/G	G/G	HWP	C	G
ss66182792	HapMap-CEU	European	118	GF	0.271	0.492	0.237		0.517	0.483

	HapMap-HCB	Asian	90	GF	0.156	0.489	0.356		0.400	0.600

	HapMap-JPT	Asian	90	GF	0.133	0.533	0.333		0.400	0.600

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.117	0.867		0.075	0.925

ss68759529	HapMap-CEU	European	120	GF	0.267	0.483	0.250		0.508	0.492

	HapMap-HCB	Asian	90	GF	0.156	0.489	0.356		0.400	0.600

	HapMap-JPT	Asian	90	GF	0.133	0.489	0.378		0.378	0.622

	HapMap-YRI	Sub-Saharan African	120	GF	0.017	0.117	0.867		0.075	0.925

ss76249606	ICMHP		8	IG	0.250	0.250	0.500		0.375	0.625

ss9837663	HapMap-CEU	European	120	IG	0.267	0.483	0.250	1.000	0.508	0.492

	HapMap-HCB	Asian	84	IG	0.167	0.500	0.333	1.000	0.417	0.583

	HapMap-JPT	Asian	86	IG	0.140	0.465	0.395	0.655	0.372	0.628

	HapMap-YRI	Sub-Saharan African	120	IG	0.017	0.117	0.867	0.251	0.075	0.925

Concordant Genotype	Total Sample	C/C	C/G	G/G
ss66182792	267	39	102	126
ss68759529	268	39	102	127
ss76249606	6	1	2	3
ss9837663	1205	142	419	621

RefSNP Genotype Summary	Total Individual	C/C	C/G	G/G
rs6429757	1212	146	429	635

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
5198	ss9837663	G/G	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	r27_ch1_JPT_affymetrix:genomewidesnp_6.0	229747
5198	ss66182792	C/G	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	chr1-HapMap-JPT
5198	ss68759529	G/G	CSHL-HAPMAP	HapMap-JPT	NA18944	JA18944	chr1-HapMap-JPT
5229	ss9837663	N/N	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	r27_ch1_JPT_affymetrix:genomewidesnp_6.0	229747
5229	ss66182792	C/G	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	chr1-HapMap-JPT
5229	ss68759529	G/G	CSHL-HAPMAP	HapMap-JPT	NA18992	JA18992	chr1-HapMap-JPT

Genotype data submitted for	1212	samples from	1212	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 .