Reference SNP(refSNP) Cluster Report: rs386994

Reference SNP(refSNP) Cluster Report: rs386994

refSNP ID: rs386994
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	80/129
Map to Genome Build:	36.3

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

HGVS Names

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss1862715 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs386994 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
ss499127	SC_JCM\|AC026713.2_25626	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	07/12/00	10/10/03	80	Genomic	unknown
ss1152016	KWOK\|OVLP-000804-463735	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	09/02/00	10/10/03	86	Genomic	99 %
ss1405106	TSC-CSHL\|TSC0261153	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	09/06/00	04/07/04	86	Genomic	95 %
ss1862715	KWOK\|OVLP-000925-19543	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	10/06/00	04/07/04	87	Genomic	99 %
ss5565094	TSC-CSHL\|TSC0641142	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	09/21/02	10/10/03	108	Genomic	unknown
ss5628133	SC_JCM\|NT_023195.10_3096986	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	01/10/03	10/10/03	111	Genomic	unknown
ss14664735	WI_SSAHASNP\|chr5.NT_006576.14_21270387	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	11/05/03	11/22/03	119	Genomic	unknown
ss23749615	PERLEGEN\|afd4514397	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	08/10/04	09/13/04	123	Genomic	unknown
ss42555058	ABI\|hCV3206530	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	07/18/05	07/18/05	126	Genomic	unknown
ss65818985	ILLUMINA\|Human1-rs386994	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	10/10/06	10/10/06	127	Genomic	unknown
ss65960632	AFFY\|SNP_A-1746130	rev/B	C/T	cttccttgttctggtggagcccatc	atcagtactttccttggaaagggtg	10/26/06	10/26/06	127	Genomic	unknown
ss66649705	ILLUMINA\|HumanHap300v1.1_rs386994	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	11/09/06	11/09/06	127	Genomic	unknown
ss67309612	ILLUMINA\|HumanHap550v1.1_rs386994	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	11/14/06	11/14/06	127	Genomic	unknown
ss67715200	ILLUMINA\|HumanHap650Yv1.0_rs386994	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	11/14/06	11/14/06	127	Genomic	unknown
ss68394266	CSHL-HAPMAP\|imsut-riken:assay:386994:11	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	01/11/07	01/11/07	127	NA	unknown
ss68394267	CSHL-HAPMAP\|perlegen:assay:25757.4514397:1	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	01/11/07	01/16/07	127	NA	unknown
ss70788262	ILLUMINA\|HumanHap550v3.0__rs386994	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	04/20/07	03/30/08	130	Genomic	unknown
ss71365385	ILLUMINA\|HumanHap650Yv3.0_rs386994	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	04/23/07	04/23/07	127	Genomic	unknown
ss75494824	ILLUMINA\|ILMN_Human_1M_rs386994	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	08/28/07	08/29/07	129	Genomic	unknown
ss79171768	ILLUMINA\|HumanHap300v2.0_rs386994	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	04/18/07	11/18/07	130	Genomic	unknown
ss81317664	HGSV\|Cor18507_SNV_20070510.chr5_38854038	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	11/26/07	11/29/07	130	Genomic	unknown
ss83443859	KRIBB_YJKIM\|KHS463078	fwd/T	A/G	ccatgcaccctttccaaggaaagtactgat	gatgggctccaccagaacaaggaagtaaac	12/04/07	12/05/07	130	Genomic	unknown
ss93067479	BCMHGSC_JDW\|JWB-1965999	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	02/26/08	03/03/08	129	Genomic	unknown
ss108973779	1000GENOMES\|CEU.trio.12.15.2008_1248132_chr5_38854038	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	12/15/08	12/16/08	130	Genomic	unknown
ss111723731	1000GENOMES\|NA19240_2008_12_16_1118427_chr5_38854038	rev/B	C/T	gtttacttccttgttctggtggagcccatc	atcagtactttccttggaaagggtgcatgg	12/16/08	12/17/08	130	Genomic	unknown

Fasta sequence (Legend)

 TTAGCTATAT TGTGTGAAGA TATTTCTAGA CCAAGGACAT CTTTAACCTG TGAATTAAAG
 TCTCTATTCA TGGCTTTTTT TTTTTCTTTA ACTATGGAGA CCTTAGGAGC TAGAGAGATA
 CAATAAAAGG AAGAAGAGTT TTTTTTTTTA ATGACATCTG CTTAAAGGAG GAGAAGTCAT
 TAGATCTATT ATCTTCCTAC atcaaccaac tataaaggta aaataaacta tttttcagat
 aaacaagatc tcaaaaaatt tacttaccat gcaccctttc caaggaaagt actgat
 R
 gatgggctcc accagaacaa ggaagtaaac caagaaagag tgaaacaaga gattcaATGC
 AAGAAAGATG TAAAGGAAGT CTCTAAATTA ATGGGAAAGG AGATTCCAAG AAAACAGTAG
 GCAATCCTAG GTATCGATCA TCCAATTAAT GTGGTCCAGA AGGTTCTAGA AGAGACATCT
 TCCaaaaagt aaaagtgata gtgtacttaa tttgtttgaa tgtataaaga ggagatttac
 agggggagtg tttggaaatt agtgataaat acatagaaaa ctaagcaaat ggaaaaacaa
 gtcagacatt cactttaggg aaagaaaatg taaggggaaa agcaatcata ttctattata
 ttactgagct ttctttgtca cttatgtatt gtcataataa catgtttact gggcactgat
 tctaagttta ctgggatggt gggtagatgg gaattgttct ctctctctct ctcaatccct
 gtatgtgtgt atgtgtaaga gagcaatatg ttcagtttcc atagaggtaa gttgatggta
 atgctaaaac agaaaaattt ttaaaaagta gcaatataaa cattttttcc agggatacgc
 aaataatata tcagaggagc tgaaaCTAAT TGCCTCTGGA AAACTGGTAA TGAGAGCAAA
 AAGAAAGGCT GCTCTTTCTC ATAAAATCTA TAGAGTTATT TGACTCTTGT CATAGGCCga
 ttctctggaa agtagattct gagatggatc caagagtttt attggggagt attcttggca
 tcaaGGAAGA GACTGGAATG AAGAACAAGG GAGCCTGTTC TTTATAGGTC AGCTCCTTTG
 GGGAGGTGGC AGGGTGGACG GTGGATCTAA GAGCAAATAG CATATTCATC ACATGGAATG
 TGTTTGTGCT CATGTCATAG AAGTTGGAGA ACAGAACCTT CAGCTCTTTT AACTTGGTTT
 CTTAAAAAAT AACATGTTAT TGTCATACAC ATGTCTTAAT TCAGTGGTTG TTCTACA

GeneView

GeneView: no link established by analysis of contig annotation
GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs386994 maps exactly once on NCBI human chromosome 5

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
5	NW_922596.1	4415417	38704903	minus	T	alt_assembly_1	Celera	Celera	view	296
5	NW_001838933.1	3112621	38770010	minus	T	alt_assembly_8	HuRef	HuRef	view	296
5	NT_006576.15	38791038	38854038	minus	T	ref_assembly	reference	reference	view	296

NCBI Resource Links

Submitter-Referenced
GenBank
NT_023195.10 AC010938 AC026713.3

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	A/A	A/G	G/G	HWP	A	G
ss1405106	AfAm	African American	30	IG	0.067	0.067	0.867	0.020	0.100	0.900

	Caucasian	European	38	IG	0.053	0.263	0.684	0.655	0.184	0.816

	Asian	Asian	38	IG		0.053	0.947	1.000	0.026	0.974

	CEPH	European	42	IG		0.190	0.810	0.655	0.095	0.905

	PDpanel	Global	48	IG	0.042	0.208	0.750	0.439	0.146	0.854

ss1862715	CEPH		184	AF					0.250	0.750

	HapMap-CEU	European	120	IG	0.050	0.283	0.667	0.527	0.192	0.808

	HapMap-HCB	Asian	90	IG		0.111	0.889	0.752	0.056	0.944

	HapMap-JPT	Asian	88	IG		0.114	0.886	0.752	0.057	0.943

	HapMap-YRI	Sub-Saharan African	120	IG	0.083	0.383	0.533	1.000	0.275	0.725

ss23749615	AFD_EUR_PANEL	European	46	IG		0.217	0.783	0.584	0.109	0.891

	AFD_AFR_PANEL	African American	46	IG		0.304	0.696	0.403	0.152	0.848

	AFD_CHN_PANEL	Asian	48	IG		0.042	0.958	1.000	0.021	0.979

Concordant Genotype	Total Sample	A/A	A/G	G/G
ss1405106	99
ss1862715	270	12	69	188
ss23749615	69

RefSNP Genotype Summary	Total Individual	A/A	A/G	G/G
rs386994	420	12	69	188

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
837	ss1405106	C/T	AFFY	AfAm	NA17106		AFFY_GENOTYPING_112103
837	ss1405106	T/T	AFFY	AfAm	NA17106		AFFY_071103
837	ss23749615	C/T	PERLEGEN	AFD_AFR_PANEL	NA17106		71_IND_CHR_5
846	ss1405106	T/T	AFFY	AfAm	NA17115		AFFY_071103
846	ss23749615	C/T	PERLEGEN	AFD_AFR_PANEL	NA17115		71_IND_CHR_5
903	ss1405106	C/T	AFFY	Caucasian	NA17208		AFFY_GENOTYPING_112103
903	ss1405106	T/T	AFFY	Caucasian	NA17208		AFFY_071103

Genotype data submitted for	452	samples from	420	individuals	Individual with multiple genotypes submission:	31

Validation Summary:

Validation status

Marker displays
Mendelian segregation

PCR results confirmed
in multiple reactions

Homozygotes detected
in individual genotype data

Validated by: ILLUMINA

DoubleHit found by: BCM_SSAHASNP, NCBI

UNKNOWN

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Revised: May 25, 2006 1:38 PM .