Reference SNP(refSNP) Cluster Report: rs10501429

Reference SNP(refSNP) Cluster Report: rs10501429

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	119/130
Map to Genome Build:	36.3

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

HGVS Names
NM_024678.3:c.260C>A
NP_078954.3:p.Thr87Asn

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss38777840 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs10501429 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
ss14894100	PERLEGEN\|PS01708625	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	11/13/03	04/07/04	119	Genomic	unknown
ss15635346	SC_SNP\|NT_033927.6_8478819	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	11/17/03	10/25/06	120	Genomic	unknown
ss19211676	CSHL-HAPMAP\|CSHL-HuDD-200402.chr11.NT_033927.6_8478819	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	02/20/04	03/04/04	120	Genomic	unknown
ss20783316	SSAHASNP\|WGSA-200403-chr11.chr11.NT_033927.6_8478819	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	03/19/04	03/19/04	121	Genomic	unknown
ss24130466	PERLEGEN\|afd1708625	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	08/10/04	09/13/04	123	Genomic	unknown
ss28510533	MGC_GENOME_DIFF\|BC007800x37541321-T8478819G	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	08/25/04	08/25/04	126	cDNA	unknown
ss38777840	ABI\|hCV7967396	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	07/16/05	11/02/06	126	Genomic	unknown
ss65724704	ILLUMINA\|Human1-rs10501429	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	10/10/06	10/10/06	127	Genomic	unknown
ss65848519	KRIBB_YJKIM\|KHS24316	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	10/17/06	12/16/06	127	Genomic	unknown
ss65987490	AFFY\|SNP_A-1752298	fwd/B	G/T	ttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaac	10/26/06	10/26/06	127	Genomic	unknown
ss66570390	ILLUMINA\|HumanHap300v1.1_rs10501429	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	11/09/06	11/09/06	127	Genomic	unknown
ss66889901	ILLUMINA\|HumanHap550v1.1_rs10501429	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	11/14/06	11/14/06	127	Genomic	unknown
ss66992276	ILLUMINA\|HumanHap650Yv1.0_rs10501429	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	11/14/06	11/14/06	127	Genomic	unknown
ss69321250	PERLEGEN\|PGP01708625	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	01/30/07	03/31/08	127	Genomic	unknown
ss70371189	ILLUMINA\|HumanHap300v2.0_rs10501429	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	04/18/07	11/18/07	127	Genomic	unknown
ss70485819	ILLUMINA\|HumanHap550v3.0__rs10501429	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	04/20/07	03/30/08	130	Genomic	unknown
ss71009976	ILLUMINA\|HumanHap650Yv3.0_rs10501429	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	04/23/07	04/23/07	127	Genomic	unknown
ss74811618	AFFY\|SNP_M-185697	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	08/09/07	08/09/07	128	Genomic	unknown
ss74916935	ILLUMINA\|ILMN_Human_1M_rs10501429	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	08/28/07	08/29/07	129	Genomic	unknown
ss84960524	KRIBB_YJKIM\|KHS860169	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	12/04/07	12/08/07	130	Genomic	unknown
ss85338516	HGSV\|Cor19129_SNV_20070510.chr11_77957438	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	12/06/07	12/09/07	130	Genomic	unknown
ss85477470	HGSV\|Cor18517_SNV_20070510.chr11_77957438	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	12/06/07	12/09/07	130	Genomic	unknown
ss88647867	BCMHGSC_JDW\|JWB-0446043	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	02/26/08	02/27/08	129	Genomic	unknown
ss97399845	HUMANGENOME_JCVI\|1103649730787	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	03/29/08	03/29/08	130	Genomic	unknown
ss106753790	BGI\|BGI_rs10501429	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	09/16/08	09/18/08	130	Genomic	unknown
ss110700196	1000GENOMES\|CEU.trio.12.15.2008_2575962_chr11_77957438	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	12/15/08	12/17/08	130	Genomic	unknown
ss114833174	1000GENOMES\|NA19240_2008_12_16_2321816_chr11_77957438	fwd/B	G/T	tgcccttgtacttccacagaactcccaaaa	ttaattctctatagtaacaaaaaacaagat	12/18/08	12/18/08	130	Genomic	unknown

Fasta sequence (Legend)

 TTACCTCTCA CTAAGCTATG TACATAAATA ATTTTTGCTA CTGCCTCTAC AGGTCATATG
 GCTTGTTTCA ATTATCTGTC ACAAATGAAA TATATTCTAA GTTTCATCTT CCTAATAATC
 ACACTTAAAA CAGATTGCTG TCTTAATTAA AGCCTAAACA GCCTCCACAA AAGTGTCAGA
 AATCATACCT TGGCATCACA ATTTCCAATA ACTTTAATTT TTTCTGCCTT CAGTTCCACA
 TTTTGCCTTT TGGATGGACT TTTTATCAGC TGCCCTTGTA CTTCCACAGA ACTCCCAAAA
 K
 TTAATTCTCT ATAGTAACAA AAAACAAGAT AAACAAGATA TCATTATATA CAACCTTCAT
 TTTAATATCA ACTTTGCAAT AAGAATATTA AAATACTTAA TGACAAAAGC TTTTACCCTT
 ATTGGGTTAA ATAATCTTCA GAATCTATGG ATAATCTGTC GTATAAATAG AGCATAAAGT
 TATAAAATGA ATTCCATAAG CTTTAAAATG GGAATAGAGT TAAGAATTTG TATAATTAAT
 TCAGAATTAA GAGGTTGTAC AATTGCCCTT ATTAAAAAGT TAGTTGGCCA AAACACTTTT

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_033927 ABBA01017400 BC007800

dbSNP Blast Analysis

UniGene Cluster ID
503389

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	G/G	G/T	T/T	HWP	G	N	T
ss14894100	AfAm	African American	12	IG	0.667	0.333		0.655	0.833		0.167

	Caucasian	European	22	IG	0.455	0.364	0.182	0.479	0.636		0.364

	Asian	Asian	12	IG	0.500	0.500		0.439	0.750		0.250

	CEPH	European	10	IG	1.000				1.000

	PDpanel	Global	48	IG	0.375	0.500	0.125	0.752	0.625		0.375

ss15635346	CHMJ	Asian	74	IG					0.662	0.081	0.257

ss24130466	AFD_EUR_PANEL	European	48	IG	0.500	0.500		0.150	0.750		0.250

	AFD_AFR_PANEL	African American	46	IG	0.609	0.348	0.043	1.000	0.783		0.217

	AFD_CHN_PANEL	Asian	48	IG	0.208	0.625	0.167	0.251	0.521		0.479

ss38777840	HapMap-CEU	European	120	IG	0.633	0.350	0.017	0.317	0.808		0.192

	HapMap-HCB	Asian	88	IG	0.273	0.500	0.227	1.000	0.523		0.477

	HapMap-JPT	Asian	90	IG	0.422	0.467	0.111	0.655	0.656		0.344

	HapMap-YRI	Sub-Saharan African	116	IG	0.517	0.414	0.069	0.752	0.724		0.276

ss65848519	KHP1		180	AF	0.344	0.467	0.189	0.752	0.578		0.422

ss69321250	HapMap-CEU	European	120	GF	0.617	0.367	0.017		0.800		0.200

	HapMap-HCB	Asian	90	GF	0.267	0.489	0.244		0.511		0.489

	HapMap-JPT	Asian	90	GF	0.422	0.467	0.111		0.656		0.344

	HapMap-YRI	Sub-Saharan African	120	GF	0.517	0.433	0.050		0.733		0.267

Concordant Genotype	Total Sample	G/G	G/T	T/T
ss14894100	52	26	21	5
ss24130466	71	31	35	5
ss38777840	1205	579	480	115
ss69321250	268	139	105	24
ss97399845	1	1

RefSNP Genotype Summary	Total Individual	G/G	G/T	T/T
rs10501429	1310	645	530	128

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
252	ss38777840	G/G	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	r27_ch11_CEU_illumina:human_1m_beadchip	83314
252	ss69321250	G/T	CSHL-HAPMAP	HapMap-CEU	NA11839	CEPH1349.13	chr11-HapMap-CEU
5293	ss38777840	G/T	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	r27_ch11_YRI_illumina:human_1m_beadchip	83314
5293	ss69321250	G/T	CSHL-HAPMAP	HapMap-YRI	NA19159	YOR056.02	chr11-HapMap-YRI

Genotype data submitted for	1331	samples from	1310	individuals	Individual with multiple genotypes submission:	282

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 .