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Reference SNP (refSNP) Cluster Report: rs899392                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.3277/1641 (1000 Genomes)
T=0.2459/30875 (TOPMED)
HGVS Names
  • CM000666.2:g.764433T>A
  • CM000666.2:g.764433T>C
  • CM000666.2:g.764433T>G
  • NC_000004.11:g.758221T>C
  • NC_000004.12:g.764433T>A
  • NC_000004.12:g.764433T>C
  • NC_000004.12:g.764433T>G
  • NM_001317836.1:c.601-551T>A
  • NM_001317836.1:c.601-551T>C
  • NM_001317836.1:c.601-551T>G
  • NM_006315.5:c.601-551T>A
  • NM_006315.5:c.601-551T>C
  • NM_006315.5:c.601-551T>G
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 ss277536541 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs899392 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
ss1330740TSC-CSHL|TSC0174614fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact09/06/0010/10/0386Genomic95 %
ss10185821BCM_SSAHASNP|chr4.NT_037622.3_748051fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact06/27/0310/10/03116Genomicunknown
ss17019165CSHL-HAPMAP|CSHL-HuAA-200402.chr4.NT_037622.3_748051byFreqfwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact02/17/0410/26/06120Genomicunknown
ss22211164SSAHASNP|WGSA-200403-chr4.chr4.NT_037622.3_748051fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact03/20/0403/21/04121Genomicunknown
ss44509627ABI|hCV1884910fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact07/19/0507/19/05126Genomicunknown
ss78870112HGSV|Cor18507_SNV_20070510.chr4_748051fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact10/19/0710/21/07129Genomicunknown
ss82784146HGSV|Cor18956_SNV_20070510.chr4_748051fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact11/30/0712/03/07130Genomicunknown
ss92436740BCMHGSC_JDW|JWB-1724298fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact02/26/0803/03/08129Genomicunknown
ss105798793BGI|BGI_rs899392fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact09/12/0806/17/09130Genomicunknown
ss1116474211000GENOMES|NA19240_2008_12_16_808932_chr4_748221fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact12/17/0812/17/08130Genomicunknown
ss116834970ILLUMINA-UK|NA18507_000000818_NCBI36.1_chr4_748221fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact01/18/0901/18/09130Genomic99 %
ss134641465ENSEMBL|ENSSNP2462250byFreqfwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact12/08/0803/07/10131Genomicunknown
ss139391077ENSEMBL|ENSSNP5960886fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact05/18/0905/18/09131Genomicunknown
ss161886331COMPLETE_GENOMICS|NA07022_36_chr4_748221fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact09/28/0909/28/09132Genomicunknown
ss162988288COMPLETE_GENOMICS|NA19240_36_chr4_748221fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact09/29/0909/29/09132Genomicunknown
ss165986715COMPLETE_GENOMICS|NA20431_36_chr4_748221fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact09/30/0909/30/09132Genomicunknown
ss197886469BUSHMAN|BUSHMAN-chr4-748220fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact02/16/1003/05/10132Genomicunknown
ss206640041BCM-HGSC-SUB|BCM_CMT_1011-990460fwd/BC/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact03/15/1003/18/10132Genomicunknown
ss2206896881000GENOMES|pilot_1_YRI_2499371_chr4_748221fwd/C/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact04/22/1004/22/10132Genomicunknown
ss2322223331000GENOMES|pilot_1_CEU_1826962_chr4_748221fwd/C/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact05/01/1005/01/10132Genomicunknown
ss2395517631000GENOMES|pilot_1_CHB+JPT_1436840_chr4_748221fwd/C/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact05/01/1005/01/10132Genomicunknown
ss277536541GMI|GMI_AK_SNP_1856753fwd/C/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact12/16/1012/16/10137Genomicunknown
ss284828319GMI|GMI_NA10851_SNP_841092fwd/C/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact12/17/1012/17/10138Genomicunknown
ss293052611PJP|SNP_2558969_chr4_748221fwd/C/Tctgcagccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaaacact01/21/1101/21/11134Genomicunknown
ss557249081TISHKOFF|snp_chr4_758221fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa11/22/1211/23/12138Genomicunknown
ss651001501SSMP|4_758221fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa12/14/1202/10/15138Genomicunknown
ss979664877EVA-GONL|EVA-GONL_rs899392fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa04/23/1404/24/14142Genomicunknown
ss1071210405JMKIDD_LAB|HGDP_WGS_chr4_758221fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa07/10/1407/11/14142Genomicunknown
ss13080563421000GENOMES|PHASE3_V1_19492676fwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa08/16/1408/16/14142Genomicunknown
ss1429737075DDI|DDI_rs899392fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa11/04/1411/05/14144Genomicunknown
ss1580377488EVA_GENOME_DK|EVA_GENOME_DK_snv_rs899392fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa02/19/1502/20/15144Genomicunknown
ss1589161833EVA_DECODE|EVA_DECODE_4_748221_6039_rs899392fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa03/02/1503/03/15144Genomicunknown
ss1609220823EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_4_758221_10811530fwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa03/04/1503/04/15144Genomicunknown
ss1652214856EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_4_758221_10811530fwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa03/04/1503/04/15144Genomicunknown
ss1800779733HAMMER_LAB|Hsieh_2061249fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa07/15/1507/15/15146Genomicunknown
ss1922894898WEILL_CORNELL_DGM|SNV:chr4:758221fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa10/16/1510/17/15147Genomicunknown
ss2022021600JJLAB|SNP2524155fwd/BC/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa08/29/1608/30/16149Genomicunknown
ss2150126650USC_VALOUEV|NC_000004.11:g.758221T>Cfwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa11/17/1611/17/16150Genomicunknown
ss2259757424HUMAN_LONGEVITY|HLI-4-764433-T-Cfwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa11/18/1611/18/16150Genomicunknown
ss2427156070TOPMED|4_758221_T/Cfwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa11/20/1611/20/16150Genomicunknown
ss2625511550SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV1596130fwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa01/06/1701/06/17151Genomicunknown
ss2705561207GRF|rs899392fwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa02/13/1702/13/17151Genomicunknown
ss2804595922GNOMAD|rs899392fwd/A/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa05/18/1705/18/17151Genomicunknown
ss2993979330SWEGEN|NC_000004.11:g.758221T>Cfwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa05/30/1705/30/17151Genomicunknown
ss3024780431BIOINF_KMB_FNS_UNIBA|4.764433T>Cfwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa07/05/1707/05/17151Genomicunknown
ss3345494246CSHL|rs899392fwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa10/02/1710/02/17151Genomicunknown
ss3418004790TOPMED|TOPMed_freeze_5?chr4:764,433-01fwd/A/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa10/04/1710/04/17151Genomicunknown
ss3418004791TOPMED|TOPMed_freeze_5?chr4:764,433-02fwd/C/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa10/04/1710/04/17151Genomicunknown
ss3418004792TOPMED|TOPMed_freeze_5?chr4:764,433-03fwd/G/Tgccgtgggagggggctggtgtggacgggcctgggtgggatggggagggaa10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs899392|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/G/T'|mol=Genomic|build=151
 TACTAAGTAG AGAAGCCCCT CTGAAAAGGC TGTAGGCCGT GCGACTCCAG CTCTGCAGCA
 TGGCGCACTG GAAAAGGCAG AACCATCCGG AGGCTGCAGG GGCTTGAGGA GGGTAGTAGG
 AGTGGGCGGG CACAGGGCTC CTGGGCGGCG ATGCTGCTGT TTGTCCACCT GTGGCTGTGC
 CACCAGGGCG ACCTGACATC CGCTCTGGAC TCGGTGGAGG TGATGTCAGT GCAGGTTCCT
 GGGTGGTGAC TAATGTGCCC CCATGCAGGG TGTTGGTGGC AGGGGGGTTC CAAGGGGGAC
 GGGAACTCCC TGTACCTTCC TCTCAATTTT GCTGTAAACC TTAAATTGTT CTTTAAAAAG
 TCTAATTTTT TTAAAAGACT GGGGAGCCTA GTGCATTTTT GCACTATGGT GAGAGGGAGG
 GACAGCCTGG ACCGGAGGTA GGGCCTGTGG GGAGAGGGTG CCCCTGGAGG CTGCAGCCGT
 GGGAGGGGGC TGGTGTGGAC
 N
 GGGCCTGGGT GGGATGGGGA GGGAAACACT TCGGCCCTAT GGGCCTCTCA GGCACCTGTG
 CCACCTGGGG AACCAGGGTG CCCGATTCCG GAGCTGTCAG GGCTGCTCAT GGGGCTGCAA
 ACCACCTCTT CCCGTTGCTC AGTACGGCAG GTGTGGTAGA CAGGGTGTGA TGGGGCCTGT
 CAAGAGAAAA AGGGTTCAGG GCAGCTGCAG GCCAGATAGG GGCGGGATGG GAGCCCACCA
 CTGCAAGGAG CTTGTGCCTG CGCCTGCACC CCCTGCAGAA ACGTCATCCC CCTAACTGGC
 ACGGGCCTGC CCTGTAATAT CTTATATGTT GCACTGGATT TCCGTTCAGC TGTGAGGTAG
 GGACCACACT CCATCTCTAG GCTGTGAGGT AGGGATGGAG GAATACATGA ACCAGCCCCC
 CCCACCCCAT CTCTAGGCAC GTTCTTGCAT GATTGGGGAG GGGCTGCAGA TTTCATACCA
 GCATCAAGGT GGCCATGTCA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_037622
dbSNP Blast Analysis

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

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss116834970YRI 2IG 1.00000000 0.500000000.50000000
ss1308056342EAS 1008AF 0.575399990.42460001
EUR 1006AF 0.695800010.30419999
AFR 1322AF 0.732199970.26780000
AMR 694AF 0.589300040.41069999
SAS 978AF 0.726000010.27399999
ss134641465ENSEMBL_Venter 2IG1.00000000 1.00000000
ENSEMBL_celera 4IG 0.500000000.50000000 0.250000000.75000000
ss139391077ENSEMBL_Watson 2IG1.00000000 1.00000000
ss161886331CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss162988288YRISub-Saharan African 2IG1.00000000 1.00000000
ss165986715PGP 2IG 1.00000000 0.500000000.50000000
ss17019165HapMap-CEUEuropean 108IG0.481481490.462962960.055555560.342782000.712962990.28703704
HapMap-HCBAsian 80IG0.224999990.550000010.224999990.583882000.500000000.50000000
HapMap-JPTAsian 80IG0.375000000.500000000.125000000.751830000.625000000.37500000
HapMap-YRISub-Saharan African 112IG0.517857130.464285700.017857140.099721000.750000000.25000000
ss220689688pilot_1_YRI_low_coverage_panel 118AF 0.745762710.25423729
ss232222333pilot_1_CEU_low_coverage_panel 120AF 0.666666690.33333334
ss239551763pilot_1_CHB+JPT_low_coverage_panel 120AF 0.566666660.43333334

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.441+/-0.1620000

  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_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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