Reference SNP(refSNP) Cluster Report: rs683

Reference SNP(refSNP) Cluster Report: rs683

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	36/130
Map to Genome Build:	36.3
Citation:	PubMed

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

HGVS Names
NM_000550.1:c.*123A>C
NM_000550.2:c.*123C>A
NT_008413.17:g.12699305C>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss61714540 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs683 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
ss688	WIAF\|WIAF-1194	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatactt	01/23/99	12/23/03	36	Genomic	unknown
ss3859305	SC_JCM\|AF001295.1_21693	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	09/25/01	10/25/06	100	Genomic	unknown
ss15535522	SC_SNP\|NT_008413.16_12699305	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	11/14/03	11/22/03	120	Genomic	unknown
ss17277964	CSHL-HAPMAP\|CSHL-HuAA-200402.chr9.NT_008413.16_12699305	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	02/17/04	03/04/04	120	Genomic	unknown
ss19798466	CSHL-HAPMAP\|CSHL-HuDD-200402.chr9.NT_008413.16_12699305	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	02/20/04	03/04/04	120	Genomic	unknown
ss22805583	SSAHASNP\|WGSA-200403-chr9.chr9.NT_008413.16_12699305	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	03/21/04	03/21/04	121	Genomic	unknown
ss24430042	PERLEGEN\|afd0864105	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	08/10/04	09/13/04	123	Genomic	unknown
ss43887276	ABI\|hCV3119206	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	07/18/05	11/03/06	126	Genomic	unknown
ss61714540	SI_EXO\|NT_008413.16_12699305	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	07/11/06	08/14/07	127	Genomic	unknown
ss67505457	ILLUMINA\|HumanHap550v1.1_rs683	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	11/14/06	11/14/06	127	Genomic	unknown
ss67867673	ILLUMINA\|HumanHap650Yv1.0_rs683	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	11/14/06	11/14/06	127	Genomic	unknown
ss68261098	ILLUMINA\|HumanHap250Sv1.0_rs683	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	12/06/06	12/07/06	127	Genomic	unknown
ss69283008	PERLEGEN\|PGP00864105	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	01/30/07	08/14/07	127	Genomic	unknown
ss70889969	ILLUMINA\|HumanHap550v3.0__rs683	rev/B	G/T	agctttgaaaagtatgcctagaactttaat	ctaacatatgcttgtattagaaagaaggta	04/20/07	03/31/08	130	Genomic	unknown
ss71482646	ILLUMINA\|HumanHap650Yv3.0_rs683	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	04/23/07	04/23/07	127	Genomic	unknown
ss75891983	ILLUMINA\|ILMN_Human_1M_rs683	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	08/28/07	08/29/07	129	Genomic	unknown
ss83344251	KRIBB_YJKIM\|KHS439375	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	12/04/07	12/04/07	130	Genomic	unknown
ss94014197	BCMHGSC_JDW\|JWB-2560937	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	02/26/08	03/05/08	129	Genomic	unknown
ss97779195	HUMANGENOME_JCVI\|1103652027573	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	03/30/08	03/30/08	130	Genomic	unknown
ss108610225	1000GENOMES\|CEU.trio.12.15.2008_2136389_chr9_12699305	fwd/T	A/C	taccttctttctaatacaagcatatgttag	attaaagttctaggcatacttttcaaagct	12/15/08	12/16/08	130	Genomic	unknown

Fasta sequence (Legend)

 TTCATCTGTC CACTTTTTGG TGATAACTAT TTTAATATTT GTCTTTTTAT TTTTATCTTC
 CTTTCCAAAT AGGTCGGGAG TTTAGTGTAC CTGAGATAAT TGCCATAGCA GTAGTTGGCG
 CTTTGTTACT GGTTGCACTC ATTTTTGGGA CTGCTTCTTA TCTGATTCGT GCCAGACGCA
 GTATGGATGA AGCTAACCAG CCTCTCCTCA CTGATCAGTA TCAATGCTAT GCTGAAGAAT
 ATGAAAAACT CCAGAATCCT AATCAGTCTG TGGTCTAACA AATGCCCTAC TCTCTTATGC
 ATTAGTATCA CAAAACCACC TGGTTGAATA TAATAGATTG AGTTATTAAC TGTATTTTCT
 TTCACTTTAT TACCTTCTTT CTAATACAAG CATATGTTAG
 M
 ATTAAAGTTC TAGGCATACT TTTCAAAGCT GGGAAGACCC TTTCAGAATC TTTTCAATGG
 GTTTTAATTT TCAGTTCTAT TTAAAATGGT GAATGACACT AAACTCCATG ATATTTAAGG
 ATAGTGTGAA GATCTTTGGC ATGATTTAAA GGTTGAGTAT GTGAAGATAT AAGTAAGTGA
 ACTACCATGC TTTGTTTACG TGTAAAGGAA AATAATGTTT GATAGTAAAT GTCCACTTAA
 AATACATGAA TGGGCATTTC TAAAATGTTA AAACATAAAC ACATTTCCAT TCATGGATAT
 TTGTCAACAG ATTTAAAGAA AACCACAGTT ATTAATTAAA GAAAATTAAT TATGTGTAGT
 TATAAACCAA TGAAATTTTG ATTAACCTTT TCAAATTAAT

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
dbSTS	GenBank
G44332	NT_008413.16 ABBA01065320 AL138753

dbSNP Blast Analysis

UniGene Cluster ID
270279

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/C	C/C	HWP	A	C
ss24430042	AFD_EUR_PANEL	European	48	IG	0.333	0.542	0.125	0.527	0.604	0.396

	AFD_AFR_PANEL	African American	46	IG	0.087	0.261	0.652	0.273	0.217	0.783

	AFD_CHN_PANEL	Asian	46	IG			1.000			1.000

ss61714540	HapMap-CEU	European	120	IG	0.483	0.417	0.100		0.692	0.308

	HapMap-HCB	Asian	90	IG		0.022	0.978		0.011	0.989

	HapMap-JPT	Asian	88	IG			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	IG		0.217	0.783		0.108	0.892

ss69283008	HapMap-CEU	European	120	GF	0.483	0.400	0.117		0.683	0.317

	HapMap-HCB	Asian	90	GF			1.000			1.000

	HapMap-JPT	Asian	90	GF			1.000			1.000

	HapMap-YRI	Sub-Saharan African	120	GF		0.217	0.783		0.108	0.892

Concordant Genotype	Total Sample	A/A	A/C	C/C
ss24430042	71	10	19	41
ss61714540	1202	147	343	646
ss69283008	265	42	54	169
ss97779195	1		1

RefSNP Genotype Summary	Total Individual	A/A	A/C	C/C
rs683	1264	156	360	698

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
151	ss61714540	A/C	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	r27_ch9_CEU_illumina:human_1m_beadchip
151	ss69283008	A/A	CSHL-HAPMAP	HapMap-CEU	NA10847	CEPH1334.02	chr9-HapMap-CEU
524	ss61714540	A/C	CSHL-HAPMAP	HapMap-CEU	NA12740	CEPH1444.02	r27_ch9_CEU_illumina:human_1m_beadchip
524	ss69283008	C/C	CSHL-HAPMAP	HapMap-CEU	NA12740	CEPH1444.02	chr9-HapMap-CEU
548	ss61714540	A/C	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	r27_ch9_CEU_illumina:human_1m_beadchip
548	ss69283008	C/C	CSHL-HAPMAP	HapMap-CEU	NA12763	CEPH1447.12	chr9-HapMap-CEU
5189	ss61714540	A/C	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	r27_ch9_CHB_illumina:human_1m_beadchip
5189	ss69283008	C/C	CSHL-HAPMAP	HapMap-HCB	NA18592	CH18592	chr9-HapMap-HCB
5238	ss61714540	C/C	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	r27_ch9_YRI_illumina:human_1m_beadchip
5238	ss69283008	A/C	CSHL-HAPMAP	HapMap-YRI	NA18503	YOR005.01	chr9-HapMap-YRI