Reference SNP (refSNP) Cluster Report: rs12847959

Reference SNP (refSNP) Cluster Report: rs12847959

RefSNP
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	121/151
Map to Genome Build:	108/Weight 1
Validation Status:
Citation:	PubMed LitVarNEW

Allele
Variation Class:	SNV: single nucleotide variation
RefSNP Alleles:	C/G/T (FWD)
Allele Origin:
Ancestral Allele:	G
Variation Viewer:	Assembly GRCh37.p13 GRCh38.p7
Clinical Significance:	NA
MAF/MinorAlleleCount:	C=0.4583/1730 (1000 Genomes) C=0.4495/56443 (TOPMED)

HGVS Names
CM000685.2:g.28774546G>C CM000685.2:g.28774546G>T NC_000023.10:g.28792663G>C NC_000023.11:g.28774546G>C NC_000023.11:g.28774546G>T NG_008292.1:g.191983G>C NG_008292.1:g.191983G>T NM_014271.3:c.-24-14774G>C NM_014271.3:c.-24-14774G>T

Links

SNP Details are organized in the following sections:

Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation 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

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

Submitter records for this RefSNP Cluster

The submission ss21020364 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12847959 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
ss21020364	SSAHASNP\|WGSA-200403-chrX.chrX.NT_011757.13_24759228	fwd/B	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	03/19/04	10/26/06	121	Genomic	unknown
ss43875978	ABI\|hCV2538197	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	07/18/05	07/18/05	126	Genomic	unknown
ss77558999	HGSV\|Cor12156_SNV_20070510.chrX_28552320	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	10/09/07	10/13/07	129	Genomic	unknown
ss94252388	BCMHGSC_JDW\|JWB-2672109	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	02/26/08	03/06/08	129	Genomic	unknown
ss112829184	1000GENOMES\|CEU.trio.12.15.2008_3853596_chrX_28702584	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	12/18/08	12/18/08	130	Genomic	unknown
ss114560304	1000GENOMES\|NA19240_2008_12_16_3487893_chrX_28702584	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	12/18/08	12/18/08	130	Genomic	unknown
ss133980822	ENSEMBL\|ENSSNP3122353	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	12/08/08	10/14/09	131	Genomic	unknown
ss144532807	ENSEMBL\|ENSSNP5927354	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	06/05/09	06/07/09	131	Genomic	unknown
ss163069693	COMPLETE_GENOMICS\|NA07022_36_chrX_28702584	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	09/29/09	09/29/09	132	Genomic	unknown
ss164651642	COMPLETE_GENOMICS\|NA19240_36_chrX_28702584	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	09/29/09	09/29/09	132	Genomic	unknown
ss166147197	COMPLETE_GENOMICS\|NA20431_36_chrX_28702584	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	09/30/09	09/30/09	132	Genomic	unknown
ss204194105	BUSHMAN\|BUSHMAN-chrX-28702583	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	02/16/10	03/10/10	132	Genomic	unknown
ss283719690	GMI\|GMI_AK_SNP_8040133	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	12/16/10	12/16/10	137	Genomic	unknown
ss287601273	GMI\|GMI_NA10851_SNP_3614092	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	12/17/10	12/17/10	138	Genomic	unknown
ss294537812	PJP\|SNP_4044170_chrX_28702584	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	01/21/11	01/21/11	134	Genomic	unknown
ss341385186	1000GENOMES\|20100804_snps_136890_chrX_28792663	fwd/	C/G	gttgagccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaaatggc	03/23/11	03/23/11	134	Genomic	unknown
ss566811150	TISHKOFF\|snp_chrX_28792663	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	11/22/12	11/23/12	138	Genomic	unknown
ss662744034	SSMP\|X_28792663	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	12/14/12	02/14/15	138	Genomic	unknown
ss1082847872	JMKIDD_LAB\|HGDP_WGS_chrX_28792663	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	07/10/14	07/12/14	142	Genomic	unknown
ss1432020519	DDI\|DDI_rs12847959	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	11/04/14	11/05/14	144	Genomic	unknown
ss1553912516	1000GENOMES\|PHASE3_chrX_686198	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	08/16/14	08/07/15	144	Genomic	unknown
ss1583356330	EVA_GENOME_DK\|EVA_GENOME_DK_snv_rs12847959	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	02/19/15	02/20/15	144	Genomic	unknown
ss1640521934	EVA_UK10K_ALSPAC\|EVA_UK10K_ALSPAC_X_28792663_45229925	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	03/04/15	03/04/15	144	Genomic	unknown
ss1683515967	EVA_UK10K_TWINSUK\|EVA_UK10K_TWINSUK_X_28792663_45229925	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	03/04/15	03/04/15	144	Genomic	unknown
ss1939232746	WEILL_CORNELL_DGM\|SNV:chrX:28792663	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	10/16/15	10/19/15	147	Genomic	unknown
ss1971358687	GENOMED\|rs12847959	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	02/16/16	02/16/16	147	Genomic	unknown
ss2158995067	USC_VALOUEV\|NC_000023.10:g.28792663G>C	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	11/17/16	11/17/16	150	Genomic	unknown
ss2316427938	HUMAN_LONGEVITY\|HLI-X-28774546-G-C	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	11/18/16	11/18/16	150	Genomic	unknown
ss2710121004	GRF\|rs12847959	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	02/13/17	02/13/17	151	Genomic	unknown
ss2977503938	GNOMAD\|rs12847959	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	05/23/17	05/23/17	151	Genomic	unknown
ss3019776508	SWEGEN\|NC_000023.10:g.28792663G>C	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	05/30/17	05/30/17	151	Genomic	unknown
ss3029025190	BIOINF_KMB_FNS_UNIBA\|X.28774546G>C	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	07/05/17	07/05/17	151	Genomic	unknown
ss3607751944	TOPMED\|TOPMed_freeze_5?chrX:28,774,546-01	fwd/	C/G	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	10/07/17	10/07/17	151	Genomic	unknown
ss3607751945	TOPMED\|TOPMed_freeze_5?chrX:28,774,546-02	fwd/	G/T	gccacctgcattttcttaccacatg	tcttttccatagggcagctctcaaa	10/07/17	10/07/17	151	Genomic	unknown

Fasta sequence (Legend)

>gnl|dbSNP|rs12847959|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/G/T'|mol=Genomic|build=151 TCTGGTTTTA CGCCTACCTC ATTActttct gatttacttt actgattctt tttttcgatt
 tgttctcatt atgttgtagt tcaagacctc aatcctgagc cctcccttat atttttccct
 ctttagatga ctgcattgag ttttttggct ttaaataaaa tctgcctgtt gatgactcct
 aaatatgtac ctgcagATTA TATTTATCTT ATATTGTTTC CATCtgtatt agttatctat
 tgctgcataa aaagttatcc aaaccttagt gtcttaataa catctattat atcatacttt
 ctgtgggtca ggaatctggg catggattat ccgggtcctc tggctcagga tctctaacaa
 ggctgcagtc aatgtattgg atggggcagc agtcatctca gggtctgatt ggggcaggac
 ccactttcag gttcactcaa taatggttta caaaattcag ttccttgaaa gttgagccac
 ctgcattttc ttaccacatg
 B
 tcttttccat agggcagctc tcaaaatggc agctggcttc atcaaagtga gtaaacgaga
 aaatgtcagc aaaaggtggg ccagtgtttt ataacttaat ctcagaaatg acataccatc
 actctggcct tattaccaag tcactaggtc catttctcac tcaaaggtgg gggattacac
 aaggtaatga ataacaagag gcaagggtca tATATGGTAT GATAAaagca tctcaaactt
 tatccaaaac aaaacgactt cctgacttcc caaactttct atgcccctag ccttcctcat
 ctcagtaaat ggtagcacaa taccccttta ctctctgacc aaacctggaa gtgatctttg
 atttctcttt tactcactaa ccatacccga tgtattagta actcatatta ttgttatcta
 caaattattc accaagtctg atgaccttcc atcattacct ttgttaaaat tgtagtctaa
 gatgatataa attcttgtct

NCBI Resource Links

Submitter-Referenced
GenBank
NT_011757

dbSNP Blast Analysis

Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here]

	Sample Ascertainment				Genotype Detail					Alleles
ss#	Population	Individual Group	Chrom. Sample Cnt.	Source	C	C/C	C/G	G/G	HWP	C	G
ss133980822	ENSEMBL_Venter		2	IG		1.00000000				1.00000000

ss144532807	ENSEMBL_Watson		2	IG		1.00000000				1.00000000

ss1553912516	EAS		1008	AF						0.34520000	0.65480000

	EUR		1006	AF						0.40059999	0.59939998

	AFR		1322	AF						0.25110000	0.74890000

	AMR		694	AF						0.36739999	0.63260001

	SAS		978	AF						0.40079999	0.59919995

ss163069693	CEU	European	1	IG	1.00000000					1.00000000

ss164651642	YRI	Sub-Saharan African	2	IG		1.00000000				1.00000000

ss166147197	PGP		1	IG	1.00000000					1.00000000

ss21020364	HapMap-CEU	European	112	IG		0.32142857	0.19642857	0.48214287	0.00100000	0.41964287	0.58035713

	HapMap-HCB	Asian	80	IG		0.42500001	0.20000000	0.37500000	0.00100000	0.52499998	0.47499999

	HapMap-JPT	Asian	80	IG		0.27500001	0.30000001	0.42500001	0.02002200	0.42500001	0.57499999

	HapMap-YRI	Sub-Saharan African	106	IG		0.22641510	0.11320755	0.66037738	0.00100000	0.28301886	0.71698111

Summary	Average Het.+/- std err:	Individual Count	Founders Count	Individual Overlap	Genotype Conflict
	0.497+/-0.042	0	0	0	0

Validation Summary:

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

Disclaimer Privacy statement

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