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Reference SNP (refSNP) Cluster Report: rs2999131                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:101/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/G (REV)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.3880/1943 (1000 Genomes)
C=0.4194/52668 (TOPMED)
HGVS Names
  • CM000663.2:g.58832146G>C
  • NC_000001.10:g.59297818G>C
  • NC_000001.11:g.58832146G>C
  • NR_034014.1:n.155+46841G>C
  • NR_034015.1:n.155+46841G>C
  • NR_108106.1:n.155+46841G>C
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

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

  GeneView back to top

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


  Submitter records for this RefSNP Cluster back to top
The submission ss275838283 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2999131 during BLAST analysis for the current build.


NCBI
Assay ID
Handle|Submitter IDValidation
Status
ss to rs
Orientation
/Strand
Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date
Update
Date
Build
Added
Molecule
Type
Freq
Warning
Ancestral
Allele
Success
Rate
ss4222538SC_JCM|AL450024.10_27009fwd/BC/Gatgtctcctttttggcttaagctaggttgatttatgtttatacttgaacttactaccaag10/15/0110/10/03101Genomicunknown
ss11365949WI_SSAHASNP|chr1.NT_032977.5_11746729rev/TC/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat07/03/0310/10/03116Genomicunknown
ss13037595SC_SNP|NT_032977.5_11746729rev/TC/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat10/22/0310/31/03119Genomicunknown
ss16459974CSHL-HAPMAP|CSHL-HuAA-200402.chr1.NT_032977.6_20860888byFreqrev/TC/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat02/17/0410/30/04120Genomicunknown
ss44049052ABI|hCV1626075rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat07/18/0507/18/05126Genomicunknown
ss81315764HGSV|Cor18507_SNV_20070510.chr1_59009839rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat11/26/0711/29/07130Genomicunknown
ss82693727HGSV|Cor19240_SNV_20070510.chr1_59009839rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat11/30/0712/03/07130Genomicunknown
ss1082299261000GENOMES|CEU.trio.12.15.2008_72043_chr1_59070406rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat12/15/0812/15/08130Genomicunknown
ss1105017081000GENOMES|NA19240_2008_12_16_68952_chr1_59070406rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat12/17/0812/17/08130Genomicunknown
ss118722349ILLUMINA-UK|NA18507_000066448_NCBI36.1_chr1_59070406rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat01/21/0901/21/09130Genomic99 %
ss161263859ENSEMBL|ENSSNP241718rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat09/24/0909/24/09131Genomicunknown
ss163423164COMPLETE_GENOMICS|NA19240_36_chr1_59070406rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat09/29/0909/29/09132Genomicunknown
ss198497007BUSHMAN|BUSHMAN-chr1-59070405rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat02/16/1003/06/10132Genomicunknown
ss2184014901000GENOMES|pilot_1_YRI_211173_chr1_59070406rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat04/22/1004/22/10132Genomicunknown
ss2305468431000GENOMES|pilot_1_CEU_151472_chr1_59070406rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat05/01/1005/01/10132Genomicunknown
ss2382392911000GENOMES|pilot_1_CHB+JPT_124368_chr1_59070406rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat05/01/1005/01/10132Genomicunknown
ss253117260BL|SNP63116_1_59070406rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat08/18/1008/18/10134Genomicunknown
ss275838283GMI|GMI_AK_SNP_158446rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat12/16/1012/16/10137Genomicunknown
ss290517466PJP|SNP_23824_chr1_59070406rev/C/Gcttggtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaaggagacat01/21/1101/21/11134Genomicunknown
ss554143715TISHKOFF|snp_chr1_59297818rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga11/22/1211/22/12138Genomicunknown
ss647991009SSMP|1_59297818rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga12/14/1202/09/15138Genomicunknown
ss975190562EVA-GONL|EVA-GONL_rs2999131rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga04/23/1404/23/14142Genomicunknown
ss1067909846JMKIDD_LAB|HGDP_WGS_chr1_59297818rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga07/10/1407/10/14142Genomicunknown
ss12910037851000GENOMES|PHASE3_V1_1734738rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga08/16/1408/16/14142Genomicunknown
ss1425818144DDI|DDI_rs2999131rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga11/04/1411/04/14144Genomicunknown
ss1574080441EVA_GENOME_DK|EVA_GENOME_DK_snv_rs2999131rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga02/19/1502/19/15144Genomicunknown
ss1584557388EVA_DECODE|EVA_DECODE_1_59070406_428133_rs2999131rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga03/02/1503/02/15144Genomicunknown
ss1600234790EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_59297818_943085rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga03/04/1503/04/15144Genomicunknown
ss1643228823EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_59297818_943085rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga03/04/1503/04/15144Genomicunknown
ss1794412154HAMMER_LAB|Hsieh_185520rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga07/15/1507/15/15146Genomicunknown
ss1918398435WEILL_CORNELL_DGM|SNV:chr1:59297818rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga10/16/1510/16/15147Genomicunknown
ss1966752611GENOMED|rs2999131rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga02/16/1602/16/16147Genomicunknown
ss2019715797JJLAB|SNP218352rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga08/29/1608/30/16149Genomicunknown
ss2147730992USC_VALOUEV|NC_000001.10:g.59297818G>Crev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga11/17/1611/17/16150Genomicunknown
ss2162735008HUMAN_LONGEVITY|HLI-1-58832146-G-Crev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga11/18/1611/18/16150Genomicunknown
ss2324977417TOPMED|1_59297818_G/Crev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga11/19/1611/19/16150Genomicunknown
ss2624371568SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV134862rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga01/06/1701/06/17151Genomicunknown
ss2697645006GRF|rs2999131rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga02/13/1702/13/17151Genomicunknown
ss2755455718GNOMAD|rs2999131rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga05/17/1705/17/17151Genomicunknown
ss2986861940SWEGEN|NC_000001.10:g.59297818G>Crev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga05/30/1705/30/17151Genomicunknown
ss3023618770BIOINF_KMB_FNS_UNIBA|1.58832146G>Crev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga07/05/1707/05/17151Genomicunknown
ss3077353361TOPMED|TOPMed_freeze_5?chr1:58,832,146rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga09/28/1709/28/17151Genomicunknown
ss3343467488CSHL|rs2999131rev/C/Gtagtaagttcaagtataaacataaatcaacctagcttaagccaaaaagga10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2999131|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/G'|mol=Genomic|build=151
 TGGCCACAGT AGGTGGACCT GAGACCCAAG GTGGGTCAAT GGTAATACCC ACTCTTAGCC
 AGGGAGATCT ATTTAAGGCA TGCACATGTC CCAAGCCAGG CCAATCAAAG GATTTCCATG
 GGACTTTTCT ACCCCGAGCT GTAGGAAGAA AATTTCTTCT CTCTCTGATC GCAAGCTGTA
 AAAATGGAAG CCTAAACTTT ACATATATTA TTATACACTA TTCTATGTAT TCCATACATA
 AGTTATATTT TACAAATTAA AAAAGACACT ACAAAAGCTG GAAGGCAAGC CTGGAGCTTT
 GGCAATCACA TGCTCATCCC ATGTAAGGAA CTCATGAAGA GAAGAGAACA ATTCCAATAT
 GCAGGAAGGC AGAGGTAACA GGCAGGGATG GTGCCCCGTA AGTGCTGGAG ACTCGGATCT
 GGCCAATTCC GATCCACCCC TACCCTTCTC ACAATTTATC TGAGCAAATA ATGTCTCCTT
 TTTGGCTTAA GCTAGGTTGA
 S
 TTTATGTTTA TACTTGAACT TACTACCAAG AAATAAAAAT AATATCTCAT ATTTTATTTA
 TGCCCTTTTT TCCACAAAGG ATTGATTTAA AGTTAACATC CTTCATTTGT CTTATAATTT
 CTGATTTATG GTTTATTACT TCACTCAAGG TGATCACTCA ATATAGTTTT CTGAGGTGAG
 CAAAGAAAGT GTAATTCGTT CATTTTACAG ATAATCTAAC TGAGGTTCAA AGAAGTAAAG
 GGACTTAGGT CACACAGCTA GCAAATGGAA GAGCCTGGAC TAGAATCTAG GTTTTCCTAT
 TTTTCTCTCT ATAATGAGAA CCTAGAATTT AGGTTCTCTT ATTTTTCTGC TAATAGATCA
 TGGCTATAAG CACTAAGAGA GAGGCTGTTG GGCTACTTGG GCTCATAAGA TTCTCATACC
 TTTCTACTGT AGGTAACTAT GCCCTTTTAA GAAGCACATC TTCATAGTAC AGTAACACTT
 GCTATAAATA TTCCTGAGAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_032977 AL136985 AL606762
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs2999131 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/G
G/G
HWPC
G
ss118722349YRI 2IG 1.00000000 1.00000000
ss1291003785EAS 1008AF 0.786700010.21329999
EUR 1006AF 0.694800020.30519998
AFR 1322AF 0.344899980.65509999
AMR 694AF 0.573499980.42649999
SAS 978AF 0.735199990.26479998
ss161263859ENSEMBL_celera 2IG 1.00000000 1.00000000
ss163423164YRISub-Saharan African 2IG 1.00000000 1.00000000
ss16459974HapMap-CEUEuropean 120IG0.550000010.366666670.083333340.654721000.733333350.26666668
HapMap-HCBAsian 90IG0.555555580.377777790.066666671.000000000.744444430.25555557
HapMap-JPTAsian 88IG0.454545470.454545470.090909091.000000000.681818190.31818181
HapMap-YRISub-Saharan African 120IG0.083333340.433333340.483333321.000000000.300000010.69999999
ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss218401490pilot_1_YRI_low_coverage_panel 118AF 0.288135590.71186441
ss230546843pilot_1_CEU_low_coverage_panel 120AF 0.699999990.30000001
ss238239291pilot_1_CHB+JPT_low_coverage_panel 120AF 0.699999990.30000001

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.475+/-0.1090000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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