Reference SNP(refSNP) Cluster Report: rs718712

Reference SNP(refSNP) Cluster Report: rs718712

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	86/137
Map to Genome Build:	37.4
Validation Status:

Allele
Variation Class:	SNV: single nucleotide variation
RefSNP Alleles:	C/T
Allele Origin:
Ancestral Allele:	C
Clinical Channel:	unknown
Clinical Significance:	NA
MAF/MinorAlleleCount:	A=0.310/677
MAF Source:	1000 Genomes

HGVS Names
NC_000020.10:g.8766008G>A
NG_028168.1:g.657713G>A
NM_015192.2:c.3112-3088G>A
NM_182734.1:c.3112-3088G>A
NT_011387.8:g.8706008G>A

Links

SNP Details are organized in the following sections:

Integrated Maps (Hint: click on 'Chr Pos' or 'Contig Pos' column value to see variation in NCBI sequence viewer)

GeneView

GeneView via analysis of contig annotation:

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

Primary Assembly Mapping
Assembly	SNP to Chr	Chr	Chr position	Contig	Contig position	Allele

RefSeqGene Mapping
RefSeqGene	Gene (ID)	SNP to RefSeqGene	Position	Allele

Gene Model(s)
Function	mRNA				Protein
Function	SNP to mRNA	Accession	Position	Allele change	Accession	Position	Residue change

Submitter records for this RefSNP Cluster

The submission ss283295586 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs718712 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
ss58929	TSC-CSHL\|TSC0042766	fwd/B	C/T	gtagtccacataccagtggcaagagcatca	cagggagcacattagaaatgtaagttctcg	09/06/00	04/07/04	86	Genomic	95 %
ss24084311	PERLEGEN\|afd4377102	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	08/10/04	09/13/04	123	Genomic	unknown
ss41365478	ABI\|hCV2229875	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	07/17/05	08/14/07	126	Genomic	unknown
ss66350123	AFFY\|SNP_A-1967649	fwd/B	C/T	agtggcaagagcatca	cagggagcacattaga	10/29/06	08/14/07	127	Genomic	unknown
ss76060986	AFFY\|AFFY_6_1M_SNP_A-1967649	fwd/B	C/T	agtggcaagagcatca	cagggagcacattaga	08/28/07	08/29/07	129	Genomic	unknown
ss81434319	KRIBB_YJKIM\|KHS60504	fwd/B	C/T	gtagtccacataccagtggcaagagcatca	cagggagcacattagaaatgtaagttctcg	11/30/07	11/30/07	130	Genomic	unknown
ss106178199	BGI\|BGI_rs718712	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	09/13/08	06/18/09	130	Genomic	unknown
ss111700193	1000GENOMES\|CEU.trio.12.15.2008_3657381_chr20_8714008	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	12/17/08	12/17/08	130	Genomic	unknown
ss117479169	ILLUMINA-UK\|NA18507_000013026_NCBI36.1_chr20_8714008	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	01/19/09	01/19/09	130	Genomic	99 %
ss167785639	COMPLETE_GENOMICS\|NA07022_36_chr20_8714008	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	09/30/09	09/30/09	132	Genomic	unknown
ss171883811	COMPLETE_GENOMICS\|NA20431_36_chr20_8714008	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	10/01/09	10/01/09	132	Genomic	unknown
ss172361630	AFFY\|GenomeWideSNP_5_SNP_A-1967649	fwd/B	C/T	agtggcaagagcatca	cagggagcacattaga	10/01/09	10/02/09	132	Genomic	unknown
ss203826652	BUSHMAN\|BUSHMAN-chr20-8714007	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	02/16/10	03/09/10	132	Genomic	unknown
ss208715508	BCM-HGSC-SUB\|BCM_CMT_1011-3196896	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	03/15/10	03/20/10	132	Genomic	unknown
ss211994838	1000GENOMES\|YRI.trio.3.2010_1456302_chr20_8714008	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	03/29/10	03/31/10	132	Genomic	unknown
ss228249953	1000GENOMES\|pilot_1_YRI_10059636_chr20_8714008	rev/	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	04/22/10	04/22/10	132	Genomic	unknown
ss237757903	1000GENOMES\|pilot_1_CEU_7362532_chr20_8714008	rev/	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	05/01/10	05/01/10	132	Genomic	unknown
ss243945457	1000GENOMES\|pilot_1_CHB+JPT_5830534_chr20_8714008	rev/	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	05/01/10	05/01/10	132	Genomic	unknown
ss255472297	BL\|SNP10597_20_8714008	rev/T	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	08/20/10	08/20/10	134	Genomic	unknown
ss283295586	GMI\|GMI_AK_SNP_7616007	rev/	A/G	cgagaacttacatttctaatgtgctccctg	tgatgctcttgccactggtatgtggactac	12/16/10	12/16/10	137	Genomic	unknown

Fasta sequence (Legend)

 ATCATTCACC TGACTTCAGA ATATTTTCTT GATTATGCCA GCATCTGCTC ACATGTGCTG
 TTTCCCTTCC GCCTACTGCC TTTATCCTCA GCAGCATCGG CCTCCAGTCA ATATTGAGAC
 TAAGCTGGAG AACTCACAGA CCTTCTGCCC ACTCAGTTCT GACTTTTATG TTGGTTTGGT
 GTCAGGCTCC ACACCACTGT CAGTGCCACA CTCCCTCCAG ACTCCCCAGA AGTTCCCTGT
 CTGCCACGTC CTTTTGCCTC CCTCTTGGCT CCCATCACAC CCCCTGCATT TGCCCTTTAC
 CCCTTGCAGA ACAAGTTTCC ACCTCCTGTG GTCCCAGAAC ACACACTTAT CTAAACTATC
 TGATTCAGCC ACGATGCAAT GGATATTTAT TAAGCACCTA CTAAATAGCA GGCACTGTTC
 TAGAAACTCT GAGCTGATGA CCTGGCTTTC TAGATCTTGC TACTCAAAGT GTAGTCCACA
 TACCAGTGGC AAGAGCATCA
 Y
 CAGGGAGCAC ATTAGAAATG TAAGTTCTCG GGCCCTACTC CAGATCAACT AAGTCAGAAT
 CTACATGTTC AACAAAATTC CCAGGAGATT TGAGTGCACA TTAGAGTTTG AAAAGCATTG
 TCTTGGTGGT TGTGGAAGAT GGAGACAATC TGGAAGAAAC CATTTCAATT TCTCTCTGCC
 CCTTCCCTTT CTAAGCCAGC CTTAGGTAAT TCTCCCCTTT GACTGCCCAG ATAACTCTGG
 GTGTTGGCCC CCTAATTGGT TTTTCCTACA GGGTATCATT TACAGACATA CCTTTTGTAT
 GTAAATATCT TATTATTGCT CCCACAAAGG GATGTCACCA TTTCAACCTT CCATTCTTAA
 TAAATGTTTA GAATCCCAGG CTCTAGACAA AATAGGCACT GAAAAAAATG ATTGTGAATG
 AAATCTTTTA AGTTTCAAAA CTACACTGGA CCCGACCTCA GCGATAGCTC TGAAAGCTCA
 CATTCAAGCC ACAGGCTGCC

NCBI Resource Links

Submitter-Referenced
GenBank
NC_000020.6

dbSNP Blast Analysis

Population Diversity

	Sample Ascertainment				Genotype Detail				Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C/C	C/T	T/T	HWP	C	T
ss117479169	YRI		2	IG		1.000			0.500	0.500

ss167785639	CEU	European	2	IG		1.000			0.500	0.500

ss171883811	PGP		2	IG		1.000			0.500	0.500

ss203826652	BANTU		2	IG		1.000			0.500	0.500

ss228249953	pilot_1_YRI_low_coverage_panel		118	AF					0.636	0.364

ss237757903	pilot_1_CEU_low_coverage_panel		120	AF					0.733	0.267

ss24084311	AFD_EUR_PANEL	European	48	IG	0.625	0.375		0.527	0.812	0.188

	AFD_AFR_PANEL	African American	46	IG	0.478	0.348	0.174	0.273	0.652	0.348

	AFD_CHN_PANEL	Asian	48	IG	0.292	0.500	0.208	1.000	0.542	0.458

ss243945457	pilot_1_CHB+JPT_low_coverage_panel		120	AF					0.650	0.350

ss41365478	HapMap-CEU	European	224	IG	0.509	0.420	0.071	0.752	0.719	0.281

	HapMap-HCB	Asian	86	IG	0.488	0.372	0.140	0.317	0.674	0.326

	HapMap-JPT	Asian	172	IG	0.465	0.419	0.116	0.752	0.674	0.326

	HapMap-YRI	Sub-Saharan African	226	IG	0.425	0.469	0.106	0.655	0.659	0.341

	HAPMAP-ASW		98	IG	0.510	0.388	0.102	0.655	0.704	0.296

	HAPMAP-CHB	Asian	82	IG	0.439	0.463	0.098	1.000	0.671	0.329

	HAPMAP-CHD		170	IG	0.353	0.541	0.106	0.200	0.624	0.376

	HAPMAP-GIH		176	IG	0.398	0.455	0.148	1.000	0.625	0.375

	HAPMAP-LWK		180	IG	0.522	0.411	0.067	0.752	0.728	0.272

	HAPMAP-MEX		100	IG	0.500	0.400	0.100	0.752	0.700	0.300

	HAPMAP-MKK		284	IG	0.458	0.415	0.127	0.439	0.665	0.335

	HAPMAP-TSI		176	IG	0.398	0.455	0.148	1.000	0.625	0.375

	ENSEMBL_Watson		2	IG	1.000				1.000

	ENSEMBL_Venter		2	IG	1.000				1.000

ss58929	AfAm	African American	12	IG	0.833	0.167			0.917	0.083

	Caucasian	European	22	IG	0.455	0.455	0.091	1.000	0.682	0.318

	Asian	Asian	12	IG	0.667	0.167	0.167		0.750	0.250

	CEPH	European	10	IG	1.000				1.000

	PDpanel	Global	40	IG	0.750	0.250		1.000	0.875	0.125

ss76060986	ICMHP		10	IG	1.000				1.000

Concordant Genotype	Total Sample	C/C	C/T	T/T
ss117479169	1
ss167785639	1
ss171883811	1
ss203826652	1
ss24084311	70
ss41365478	1200
ss58929	49	35	12	2
ss76060986	5	5

RefSNP Genotype Summary	Total Individual	C/C	C/T	T/T
rs718712	1316	40	12	2

Discordant Genotypes:
Indiviudal SampleID	SubSNP(ss)	Genotype	Population Handle	Submitter Population	Submitter SampleID	SampleID Alias	Submission Batch	NCBI ProbeID
215	ss24084311	A/G	PERLEGEN	AFD_EUR_PANEL	NA10857		71_IND_CHR_20
215	ss41365478	N/N	CSHL-HAPMAP	HapMap-CEU	NA10857	CEPH1346.01	r27_ch20_CEU_affymetrix:genomewidesnp_6.0
374	ss41365478	A/A	CSHL-HAPMAP	HapMap-CEU	NA12234	CEPH1375.12	r27_ch20_CEU_affymetrix:genomewidesnp_6.0
620	ss41365478	A/G	CSHL-HAPMAP	HapMap-CEU	NA12874	CEPH1459.11	r27_ch20_CEU_affymetrix:genomewidesnp_6.0
5137	ss41365478	A/G	CSHL-HAPMAP	HapMap-YRI	NA19131	YOR101.02	r27_ch20_YRI_affymetrix:genomewidesnp_6.0
5168	ss41365478	G/G	CSHL-HAPMAP	HapMap-HCB	NA18555	CH18555	r27_ch20_CHB_affymetrix:genomewidesnp_6.0
5231	ss41365478	G/G	CSHL-HAPMAP	HapMap-JPT	NA18998	JA18998	r27_ch20_JPT_affymetrix:genomewidesnp_6.0
5263	ss41365478	G/G	CSHL-HAPMAP	HapMap-YRI	NA18861	YOR024.02	r27_ch20_YRI_affymetrix:genomewidesnp_6.0
5283	ss41365478	N/N	CSHL-HAPMAP	HapMap-YRI	NA19205	YOR048.01	r27_ch20_YRI_affymetrix:genomewidesnp_6.0
5301	ss41365478	G/G	CSHL-HAPMAP	HapMap-YRI	NA19142	YOR071.01	r27_ch20_YRI_affymetrix:genomewidesnp_6.0

Genotype data submitted for	1338	samples from	1316	individuals	Individual with multiple genotypes submission:	22

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

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GeneView via analysis of contig annotation:

GeneView via analysis of contig annotation: N/A.

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

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