NCBI
dbSNP
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This legacy RefSNP page contains old data from dbSNP build 151 (March 2018) and is no longer maintained. Please update your links and bookmarks to use the re-designed RefSNP Report page.
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Reference SNP (refSNP) Cluster Report: rs1489396                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:88/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqbySubmitterwith2hitWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.3792/1899 (1000 Genomes)
G=0.3869/48587 (TOPMED)
HGVS Names
  • CM000663.2:g.78936569G>A
  • NC_000001.10:g.79402254G>A
  • NC_000001.11:g.78936569G>A
  • NM_022159.3:c.761-158C>T
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 ss275889840 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1489396 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
ss2315076TSC-CSHL|TSC0721857byFreqfwd/BC/Tttaaaacttgagtcagatttttaacatataattacattgtccaaacacattaagaatgtt10/20/0004/07/0488Genomic95 %
ss9841858BCM_SSAHASNP|chr1.NT_004483.15_1071325rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa06/27/0310/10/03116Genomicunknown
ss46536147PERLEGEN|PS01057184rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa08/01/0508/01/05126Genomicunknown
ss65715861ILLUMINA|Human1-rs1489396fwd/BC/Tttaaaacttgagtcagatttttaacatataattacattgtccaaacacattaagaatgtt10/10/0610/10/06127Genomicunknown
ss74861741ILLUMINA|ILMN_Human_1M_rs1489396fwd/BC/Tttaaaacttgagtcagatttttaacatataattacattgtccaaacacattaagaatgtt08/28/0708/29/07129Genomicunknown
ss84371318HGSV|Cor18555_SNV_20070510.chr1_79114275rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa11/27/0712/07/07130Genomicunknown
ss87562655BCMHGSC_JDW|JWB-0071471rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa02/26/0802/26/08129Genomicunknown
ss106579489BGI|BGI_rs1489396rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa09/16/0806/16/09130Genomicunknown
ss1083381881000GENOMES|CEU.trio.12.15.2008_98490_chr1_79174842rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa12/15/0812/15/08130Genomicunknown
ss118830204ILLUMINA-UK|NA18507_000090907_NCBI36.1_chr1_79174842rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa01/21/0901/21/09130Genomic99 %
ss119395147KRIBB_YJKIM|KHS1557394fwd/BC/Tttaaaacttgagtcagatttttaacatataattacattgtccaaacacattaagaatgtt02/04/0902/04/09131Genomicunknown
ss120244570ILLUMINA|GS0006561-OPA_rs1489396-116.3_T_R_2020rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa03/17/0903/17/09131Genomicunknown
ss138014034ENSEMBL|ENSSNP6840358rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa05/15/0905/16/09131Genomicunknown
ss155226900GMI|GMI_SNP_35864379rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa06/24/0906/24/09131Genomicunknown
ss172537814ILLUMINA|Human1M-Duov3_B_rs1489396-128_T_R_1513890344rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa10/01/0910/02/09132Genomicunknown
ss198664114BUSHMAN|BUSHMAN-chr1-79174841byFreqrev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa02/16/1009/05/14132Genomicunknown
ss2105653381000GENOMES|YRI.trio.3.2010_39974_chr1_79174842rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa03/29/1003/29/10132Genomicunknown
ss2184742441000GENOMES|pilot_1_YRI_283927_chr1_79174842rev/A/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa04/22/1004/22/10132Genomicunknown
ss2305996661000GENOMES|pilot_1_CEU_204295_chr1_79174842rev/A/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa05/01/1005/01/10132Genomicunknown
ss2382798211000GENOMES|pilot_1_CHB+JPT_164898_chr1_79174842rev/A/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa05/01/1005/01/10132Genomicunknown
ss244255346ILLUMINA|Linkage_12_rs1489396rev/TA/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa06/09/1006/09/10132Genomicunknown
ss275889840GMI|GMI_AK_SNP_210003rev/A/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa12/16/1012/16/10137Genomicunknown
ss284079591GMI|GMI_NA10851_SNP_92357rev/A/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa12/17/1012/17/10138Genomicunknown
ss290544555PJP|SNP_50913_chr1_79174842rev/A/Gaacattcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagttttaa01/21/1101/21/11134Genomicunknown
ss536880923ILLUMINA|HumanOmni5-4v1_B_rs1489396-131_T_R_1909646148rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt06/22/1208/28/15146Genomicunknown
ss648153124SSMP|1_79402254rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt12/14/1202/09/15138Genomicunknown
ss975331459EVA-GONL|EVA-GONL_rs1489396rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt04/23/1404/23/14142Genomicunknown
ss1068017879JMKIDD_LAB|HGDP_WGS_chr1_79402254rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt07/10/1407/10/14142Genomicunknown
ss12915469751000GENOMES|PHASE3_V1_2300786rev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt08/16/1408/16/14142Genomicunknown
ss1425864861DDI|DDI_rs1489396rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt11/04/1411/04/14144Genomicunknown
ss1574171675EVA_GENOME_DK|EVA_GENOME_DK_snv_rs1489396rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt02/19/1502/19/15144Genomicunknown
ss1584704816EVA_DECODE|EVA_DECODE_1_79174842_575563_rs1489396rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt03/02/1503/02/15144Genomicunknown
ss1600518939EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_1_79402254_1255622rev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt03/04/1503/04/15144Genomicunknown
ss1643512972EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_1_79402254_1255622rev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt03/04/1503/04/15144Genomicunknown
ss1712346029EVA_SVP|EVA_SVP_40581rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt03/12/1503/12/15144Genomicunknown
ss1918535392WEILL_CORNELL_DGM|SNV:chr1:79402254rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt10/16/1510/16/15147Genomicunknown
ss1966786432GENOMED|rs1489396rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt02/16/1602/16/16147Genomicunknown
ss2019788170JJLAB|SNP290725rev/TA/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt08/29/1608/30/16149Genomicunknown
ss2147803902USC_VALOUEV|NC_000001.10:g.79402254G>Arev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt11/17/1611/17/16150Genomicunknown
ss2163878571HUMAN_LONGEVITY|HLI-1-78936569-G-Arev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt11/18/1611/18/16150Genomicunknown
ss2624404741SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV180082rev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt01/06/1701/06/17151Genomicunknown
ss2697724077GRF|rs1489396rev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt02/13/1702/13/17151Genomicunknown
ss2757021920GNOMAD|rs1489396rev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt05/17/1705/17/17151Genomicunknown
ss2987075492SWEGEN|NC_000001.10:g.79402254G>Arev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt05/30/1705/30/17151Genomicunknown
ss3023655977BIOINF_KMB_FNS_UNIBA|1.78936569G>Arev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt07/05/1707/05/17151Genomicunknown
ss3343528653CSHL|rs1489396rev/A/Gtcttaatgtgtttggacaatgtaattatatgttaaaaatctgactcaagt10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1489396|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 TGCAAATTCA TACTTAAAAT ATTCAGAATC TTGTATCAAA TTGAGGATCC CTATAAACTT
 TTTCTGAGGA AGCAAGGTAA GTTAGCTGAA ATAATCACTG CAGACATCTT TATTGCATTT
 TCTGGTTGGC ATTCTGCTGT GCAACAGCAG ATTTACAAAA ATCTCATCAG GATTCATCGT
 TTACTCTAAA TCAAAGTTTC AAGCATTATG ACTAATATAT AGGTGCTCTA TATTTTTATA
 ATGTTTCTGC ATGAAAATGG TGATAATACA GCAGGTCAAA GGAATTATCA CTCAAACGTT
 TAATTAAATC ACTCATTAGT AAGTTGTAGA CACTATTCTG TAAGCCATTG TAGTTGCTTA
 TCTTTGCTTT AGTAATTATA ATTTTATAGC TTGCTTGGTT ACATACACAT ATTATATTTT
 ATTTAATGCA AAAAAAGTTA AACCATGAGT GCCATAGTGA AATTAAAAAA TTAAAACTTG
 AGTCAGATTT TTAACATATA
 Y
 ATTACATTGT CCAAACACAT TAAGAATGTT CACTCTACTT GTTATAAATA ATTTAAAACA
 CAATAATGAT GGATGAAATT GTCTCTAAGC TAATATATTT ATGATGTATA TTGATTAAAG
 TAATTTCACT TTTTTTATTT TCATGGTTTT GTTTCAGCTC TCAAAGTTTT CTTTTTTGAT
 TCATATAACA TGAAACATAT TCATCCTCAT ATGAATATGG ATGGAGACTA CATAAATATA
 TTTCCAAAGA GAAAAGCTGC ATATGATTCA AATGGTAGGA CTTTAACAAT CTAACAGACA
 ATATATCAAT GAATTTGCAA TAAATATTTA TCATGCATTT GATTATGTCA TATGTACATG
 TAACATGTGG TTTCCTATAA AAACATTTGA TGTATGTACA GTATACAGAA TATCCATATT
 CTTTTTTTTT TTTTTTTTTT TTTTTGAGAC GGAGTCTCGC TCTGTGGCCC AGGCGGGAGT
 GCAGTGGCGC AATCTCGGCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_004483
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs1489396 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss118830204YRI 2IG 1.00000000 0.500000000.50000000
ss1291546975EAS 1008AF 0.295600030.70440000
EUR 1006AF 0.380699990.61930001
AFR 1322AF 0.506100000.49390000
AMR 694AF 0.315600010.68440002
SAS 978AF 0.337399990.66260004
ss138014034ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss198664114BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
BANTU 2IG 1.00000000 0.500000000.50000000
ss218474244pilot_1_YRI_low_coverage_panel 118AF 0.508474590.49152541
ss230599666pilot_1_CEU_low_coverage_panel 120AF 0.324999990.67500001
ss2315076CEPH 184AF 0.410000030.58999997
HapMap-CEUEuropean 226IG0.123893800.433628320.442477880.751830000.340707960.65929204
HapMap-HCBAsian 86IG0.046511630.418604640.534883740.527089000.255813960.74418604
HapMap-JPTAsian 170IG0.058823530.447058830.494117650.342782000.282352950.71764708
HapMap-YRISub-Saharan African 210IG0.209523810.523809550.266666680.654721000.471428570.52857143
HAPMAP-ASW 96IG0.187500000.500000000.312500001.000000000.437500000.56250000
HAPMAP-CHBAsian 82IG0.048780490.317073170.634146331.000000000.207317070.79268295
HAPMAP-CHD 168IG0.059523810.416666660.523809550.583882000.267857130.73214287
HAPMAP-GIH 176IG0.113636370.375000000.511363630.317310000.301136370.69886363
HAPMAP-LWK 176IG0.284090910.534090940.181818190.479500000.551136370.44886363
HAPMAP-MKK 284IG0.373239430.436619730.190140840.250592000.591549280.40845069
HAPMAP-TSI 174IG0.126436780.494252860.379310340.654721000.373563230.62643677
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss238279821pilot_1_CHB+JPT_low_coverage_panel 120AF 0.283333330.71666664

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.471+/-0.1170000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqbySubmitterwith2hitWith1000GenomeData
Validated by: ILLUMINAPERLEGEN
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN