Reference SNP(refSNP) Cluster Report: rs231915

Reference SNP(refSNP) Cluster Report: rs231915

refSNP ID: rs231915
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	79/129
Map to Genome Build:	36.3

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

HGVS Names
NM_000218.2:c.1515-41059G>A
NM_181798.1:c.1134-41059G>A
NT_009237.17:g.1536256G>A

Links

, Linkout

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss78755738 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs231915 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
ss299782	KWOK\|OVLP-000621-313901	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	06/30/00	10/10/03	79	Genomic	97 %
ss532286	SC_JCM\|U90095.1_39705	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	07/12/00	10/10/03	89	Genomic	unknown
ss1008000	KWOK\|OVLP-000804-155169	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	09/02/00	10/10/03	89	Genomic	97 %
ss1647690	KWOK\|OVLP-000925-558070	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	10/04/00	05/16/04	89	Genomic	97 %
ss3222551	YUSUKE\|IMS-JST032635	rev/T	A/G	agacagagcccaggattccacaacggtgtc	atgtacaacaccaagcacctggcctggtgt	09/05/01	10/10/03	100	Genomic	unknown
ss15898332	SC_SNP\|NT_009237.16_1512955	rev/T	A/G	agacagagcccaggattccacaacggtgtc	atgtacaacaccaagcacctggcctggtgt	11/17/03	11/22/03	120	Genomic	unknown
ss20751201	SSAHASNP\|WGSA-200403-chr11.chr11.NT_009237.16_1512955	rev/T	A/G	agacagagcccaggattccacaacggtgtc	atgtacaacaccaagcacctggcctggtgt	03/19/04	03/19/04	121	Genomic	unknown
ss23632587	PERLEGEN\|afd0605701	rev/T	A/G	agacagagcccaggattccacaacggtgtc	atgtacaacaccaagcacctggcctggtgt	08/10/04	09/13/04	123	Genomic	unknown
ss38725994	ABI\|hCV3075792	rev/T	A/G	agacagagcccaggattccacaacggtgtc	atgtacaacaccaagcacctggcctggtgt	07/16/05	11/02/06	126	Genomic	unknown
ss66158064	AFFY\|SNP_A-2155585	rev/T	A/G	attccacaacggtgtc	atgtacaacaccaagc	10/27/06	08/14/07	127	Genomic	unknown
ss67246209	ILLUMINA\|HumanHap550v1.1_rs231915	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	11/14/06	11/14/06	127	Genomic	unknown
ss67643318	ILLUMINA\|HumanHap650Yv1.0_rs231915	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	11/14/06	11/14/06	127	Genomic	unknown
ss68202421	ILLUMINA\|HumanHap250Sv1.0_rs231915	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	12/06/06	12/07/06	127	Genomic	unknown
ss69306737	PERLEGEN\|PGP00605701	rev/T	A/G	agacagagcccaggattccacaacggtgtc	atgtacaacaccaagcacctggcctggtgt	01/30/07	08/14/07	127	Genomic	unknown
ss70724540	ILLUMINA\|HumanHap550v3.0__rs231915	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	04/20/07	03/30/08	130	Genomic	unknown
ss71293228	ILLUMINA\|HumanHap650Yv3.0_rs231915	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	04/23/07	04/23/07	127	Genomic	unknown
ss74934091	ILLUMINA\|ILMN_Human_1M_rs231915	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	08/28/07	08/29/07	129	Genomic	unknown
ss76196784	AFFY\|AFFY_6_1M_SNP_A-2155585	rev/T	A/G	attccacaacggtgtc	atgtacaacaccaagc	08/28/07	08/30/07	129	Genomic	unknown
ss78755738	HGSV\|Cor12878_SNV_20070510.chr11_2705591	rev/T	A/G	agacagagcccaggattccacaacggtgtc	atgtacaacaccaagcacctggcctggtgt	10/17/07	10/20/07	129	Genomic	unknown
ss83395461	KRIBB_YJKIM\|KHS451463	fwd/B	C/T	acaccaggccaggtgcttggtgttgtacat	gacaccgttgtggaatcctgggctctgtct	12/04/07	12/04/07	130	Genomic	unknown
ss85115457	HGSV\|Cor19240_SNV_20070510.chr11_2705591	rev/T	A/G	agacagagcccaggattccacaacggtgtc	atgtacaacaccaagcacctggcctggtgt	11/30/07	12/08/07	130	Genomic	unknown
ss88432217	BCMHGSC_JDW\|JWB-0364449	rev/T	A/G	agacagagcccaggattccacaacggtgtc	atgtacaacaccaagcacctggcctggtgt	02/26/08	02/27/08	129	Genomic	unknown

Fasta sequence (Legend)

 GGTGAGGCCT GTGTGAGGGG AGGACAGAAC CATCGGAAGT CCTGGAAGGG ATTTGTGCAA
 AGGCCCTGGG CAAGAACACT CTGGAAGGAG CTGAAGGACG AGGAGAAGGC CAGAGTGGCT
 GGGGAGGGAG GAGGGGAACA GGGAGGCAAT GAGGCTGGGA GGTGAGCGGG AGCGGTCACA
 TGAACCTCAC GCAGGGTAAG AGGGTTAGAT TTTGCACCAC ATATGATGGA AATGAAGCGC
 TTTGACTAGC GCGGCCCCGG GGGCCATCAG ATGCTCCCTC TGCCTCCACA GCAAAGCCCC
 ACAGTGCCCA CAGAGGAACG AATGCCTGGC CACGTCCCTG CCCCTTCATA GTGCAAGACG
 AGCCCACACC AGGCCAGGTG CTTGGTGTTG TACAT
 Y
 GACACCGTTG TGGAATCCTG GGCTCTGTCT GCTCGCCCTT CTGCATACAG CCCTTCTCCA
 TTCAGCTCAC TCTGCCCTAG GAGGCTGATC TCTGCAGGTT ATGTCCACAA GCTCCTGGCC
 CAGGGCTTCA GATTGGGTCT AGCCAACTGG ACCCCTGGCA GGAGGCAAGG AGGGAGGAGA
 GCGGATCCGG GGTGTCTGCT CCTGCTCCCT GCCGTGGAGC TGCTGGGGCC AGTTGTGAGC
 CTCATGTCAG ACAGCCATCA TTCTGTTAAG CTCAGGCAAC CTCCTCCTCC TCTTTATTCC
 TCGAGTCTGG GGTAGGATTT CCCCCAGGGA CACTACCCCA TGTTCCTGCA CAAGGCCTGG
 TGGTCCCTGA CACCTGACTC ACACAGGAAT GATCCTTGGG TGCCGTCCTG CGCCCCACAC
 GTAGCTACCG TGATTGTCCC TGTTTTACAG ATGAAGAAAC AGAACCTCAG AGAGGGCTTG
 AGCTGCCCTG GGCCCCTGAG

GeneView

GeneView via analysis of contig annotation: KCNQ1 potassium voltage-gated channel, KQT-like subfamily, member 1

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_009237->NM_000218

function

reference

NT_009237->NM_181798

function

HuRef

NW_001838018->NM_181798

function

Celera

NW_924962->NM_000218

function

Celera

NW_924962->NM_181798

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_009237->NM_000218->NP_000209	1536256	forward	intron

reference	NT_009237->NM_181798->NP_861463	1536256	forward	intron

HuRef	NW_001838018->NM_181798->NP_861463	1473089	reverse	intron

Celera	NW_924962->NM_000218->NP_000209	2363614	forward	intron

Celera	NW_924962->NM_181798->NP_861463	2363614	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs231915 maps exactly once on NCBI human chromosome 11

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
11	NW_001838018.2	1473089	2537595	plus	T	alt_assembly_8	HuRef	HuRef	view	395
11	NT_009237.17	1536256	2705591	minus	G	ref_assembly	reference	reference	view	395
11	NW_924962.1	2363614	2783858	minus	A	alt_assembly_1	Celera	Celera	view	395

NCBI Resource Links

Submitter-Referenced
GenBank
U90095 AC021424 U90095.1

dbSNP Blast Analysis
GenBank HTGS Finished:
AC021424.6 NC_000011.8 U90095.1

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	N	T
ss1647690	CEPH		184	AF					0.290		0.710

	HapMap-CEU	European	120	IG	0.167	0.417	0.417	0.254	0.375		0.625

	HapMap-HCB	Asian	90	IG	0.022	0.378	0.600	0.150	0.211		0.789

	HapMap-JPT	Asian	90	IG	0.156	0.378	0.467	0.251	0.344		0.656

	HapMap-YRI	Sub-Saharan African	120	IG	0.183	0.383	0.433	0.200	0.375		0.625

	CHMJ	Asian	74	IG					0.284	0.014	0.703

ss23632587	AFD_EUR_PANEL	European	48	IG	0.125	0.417	0.458	1.000	0.333		0.667

	AFD_AFR_PANEL	African American	46	IG	0.174	0.478	0.348	1.000	0.413		0.587

	AFD_CHN_PANEL	Asian	48	IG	0.125	0.375	0.500	0.584	0.312		0.688

ss38725994	AoD_African_American		90	AF					0.330		0.670

	AoD_Caucasian		92	AF					0.310		0.690

	AoD_Chinese		90	AF					0.290		0.710

	AoD_Japanese		90	AF					0.330		0.670

ss66158064	HapMap-CEU	European	118	GF	0.102	0.492	0.407		0.347		0.653

	HapMap-HCB	Asian	90	GF	0.022	0.400	0.578		0.222		0.778

	HapMap-JPT	Asian	90	GF	0.111	0.444	0.444		0.333		0.667

	HapMap-YRI	Sub-Saharan African	120	GF	0.150	0.433	0.417		0.367		0.633

ss69306737	HapMap-CEU	European	120	GF	0.167	0.417	0.417		0.375		0.625

	HapMap-HCB	Asian	90	GF	0.022	0.378	0.600		0.211		0.789

	HapMap-JPT	Asian	90	GF	0.156	0.378	0.467		0.344		0.656

	HapMap-YRI	Sub-Saharan African	120	GF	0.183	0.383	0.433		0.375		0.625

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss1647690	252	29	109	114
ss23632587	70
ss66158064	251
ss69306737	252

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs231915	332	29	109	114

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
169	ss1647690	C/C	CSHL-HAPMAP	HapMap-CEU	NA06994	CEPH1340.09	r23_ch11_CEU_affymetrix:genechip500k	4518985
169	ss66158064	A/G	CSHL-HAPMAP	HapMap-CEU	NA06994	CEPH1340.09	chr11-HapMap-CEU
169	ss69306737	G/G	CSHL-HAPMAP	HapMap-CEU	NA06994	CEPH1340.09	chr11-HapMap-CEU
199	ss1647690	C/C	CSHL-HAPMAP	HapMap-CEU	NA12056	CEPH1344.12	r23_ch11_CEU_affymetrix:genechip500k	4518985
199	ss66158064	A/G	CSHL-HAPMAP	HapMap-CEU	NA12056	CEPH1344.12	chr11-HapMap-CEU
199	ss69306737	G/G	CSHL-HAPMAP	HapMap-CEU	NA12056	CEPH1344.12	chr11-HapMap-CEU
242	ss1647690	T/T	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	r23_ch11_CEU_affymetrix:genechip500k	4518985
242	ss23632587	A/A	PERLEGEN	AFD_EUR_PANEL	NA10854		71_IND_CHR_11
242	ss66158064	A/G	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	chr11-HapMap-CEU
242	ss69306737	A/A	CSHL-HAPMAP	HapMap-CEU	NA10854	CEPH1349.02	chr11-HapMap-CEU
345	ss1647690	C/C	CSHL-HAPMAP	HapMap-CEU	NA12717	CEPH1358.12	r23_ch11_CEU_affymetrix:genechip500k	4518985
345	ss66158064	A/G	CSHL-HAPMAP	HapMap-CEU	NA12717	CEPH1358.12	chr11-HapMap-CEU
345	ss69306737	G/G	CSHL-HAPMAP	HapMap-CEU	NA12717	CEPH1358.12	chr11-HapMap-CEU
408	ss1647690	C/C	CSHL-HAPMAP	HapMap-CEU	NA12154	CEPH1408.10	r23_ch11_CEU_affymetrix:genechip500k	4518985
408	ss66158064	A/G	CSHL-HAPMAP	HapMap-CEU	NA12154	CEPH1408.10	chr11-HapMap-CEU
408	ss69306737	G/G	CSHL-HAPMAP	HapMap-CEU	NA12154	CEPH1408.10	chr11-HapMap-CEU
429	ss1647690	C/C	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	r23_ch11_CEU_affymetrix:genechip500k	4518985
429	ss66158064	A/G	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr11-HapMap-CEU
429	ss69306737	G/G	CSHL-HAPMAP	HapMap-CEU	NA10835	CEPH1416.01	chr11-HapMap-CEU
439	ss1647690	C/T	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	r23_ch11_CEU_affymetrix:genechip500k	4518985
439	ss66158064	A/A	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	chr11-HapMap-CEU
439	ss69306737	A/G	CSHL-HAPMAP	HapMap-CEU	NA12249	CEPH1416.12	chr11-HapMap-CEU
565	ss1647690	T/T	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	r23_ch11_CEU_affymetrix:genechip500k	4518985
565	ss66158064	A/G	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	chr11-HapMap-CEU
565	ss69306737	A/A	CSHL-HAPMAP	HapMap-CEU	NA12801	CEPH1454.01	chr11-HapMap-CEU
579	ss1647690	T/T	CSHL-HAPMAP	HapMap-CEU	NA12815	CEPH1454.15	r23_ch11_CEU_affymetrix:genechip500k	4518985
579	ss66158064	A/G	CSHL-HAPMAP	HapMap-CEU	NA12815	CEPH1454.15	chr11-HapMap-CEU
579	ss69306737	A/A	CSHL-HAPMAP	HapMap-CEU	NA12815	CEPH1454.15	chr11-HapMap-CEU
5168	ss1647690	T/T	CSHL-HAPMAP	HapMap-HCB	NA18555	CH18555	r23_ch11_HCB_affymetrix:genechip500k	4518985
5168	ss66158064	A/G	CSHL-HAPMAP	HapMap-HCB	NA18555	CH18555	chr11-HapMap-HCB
5168	ss69306737	A/A	CSHL-HAPMAP	HapMap-HCB	NA18555	CH18555	chr11-HapMap-HCB
5214	ss1647690	C/C	CSHL-HAPMAP	HapMap-JPT	NA18966	JA18966	r23_ch11_JPT_affymetrix:genechip500k	4518985
5214	ss66158064	A/G	CSHL-HAPMAP	HapMap-JPT	NA18966	JA18966	chr11-HapMap-JPT
5214	ss69306737	G/G	CSHL-HAPMAP	HapMap-JPT	NA18966	JA18966	chr11-HapMap-JPT
5221	ss1647690	C/C	CSHL-HAPMAP	HapMap-JPT	NA18995	JA18995	r23_ch11_JPT_affymetrix:genechip500k	4518985
5221	ss66158064	A/G	CSHL-HAPMAP	HapMap-JPT	NA18995	JA18995	chr11-HapMap-JPT
5221	ss69306737	G/G	CSHL-HAPMAP	HapMap-JPT	NA18995	JA18995	chr11-HapMap-JPT
5232	ss1647690	T/T	CSHL-HAPMAP	HapMap-JPT	NA19000	JA19000	r23_ch11_JPT_affymetrix:genechip500k	4518985
5232	ss66158064	A/G	CSHL-HAPMAP	HapMap-JPT	NA19000	JA19000	chr11-HapMap-JPT
5232	ss69306737	A/A	CSHL-HAPMAP	HapMap-JPT	NA19000	JA19000	chr11-HapMap-JPT
5253	ss1647690	C/T	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	r23_ch11_YRI_affymetrix:genechip500k	4518985
5253	ss66158064	A/A	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	chr11-HapMap-YRI
5253	ss69306737	A/G	CSHL-HAPMAP	HapMap-YRI	NA18872	YOR017.01	chr11-HapMap-YRI
5261	ss1647690	T/T	CSHL-HAPMAP	HapMap-YRI	NA18856	YOR023.03	r23_ch11_YRI_affymetrix:genechip500k	4518985
5261	ss66158064	A/G	CSHL-HAPMAP	HapMap-YRI	NA18856	YOR023.03	chr11-HapMap-YRI
5261	ss69306737	A/A	CSHL-HAPMAP	HapMap-YRI	NA18856	YOR023.03	chr11-HapMap-YRI
5267	ss1647690	C/C	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	r23_ch11_YRI_affymetrix:genechip500k	4518985
5267	ss66158064	A/G	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	chr11-HapMap-YRI
5267	ss69306737	G/G	CSHL-HAPMAP	HapMap-YRI	NA18913	YOR028.03	chr11-HapMap-YRI
5268	ss1647690	C/T	CSHL-HAPMAP	HapMap-YRI	NA19094	YOR040.01	r23_ch11_YRI_affymetrix:genechip500k	4518985
5268	ss66158064	G/G	CSHL-HAPMAP	HapMap-YRI	NA19094	YOR040.01	chr11-HapMap-YRI
5268	ss69306737	A/G	CSHL-HAPMAP	HapMap-YRI	NA19094	YOR040.01	chr11-HapMap-YRI
5308	ss1647690	C/C	CSHL-HAPMAP	HapMap-YRI	NA19143	YOR074.02	r23_ch11_YRI_affymetrix:genechip500k	4518985
5308	ss66158064	A/G	CSHL-HAPMAP	HapMap-YRI	NA19143	YOR074.02	chr11-HapMap-YRI
5308	ss69306737	G/G	CSHL-HAPMAP	HapMap-YRI	NA19143	YOR074.02	chr11-HapMap-YRI

Genotype data submitted for	341	samples from	332	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

Validated by: PERLEGEN

DoubleHit found by: BCM_SSAHASNP

UNKNOWN

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Revised: May 25, 2006 1:38 PM .