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Reference SNP (refSNP) Cluster Report: rs149485401                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:134/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:T=0.0088/886 (ExAC)
T=0.0050/25 (1000 Genomes)
T=0.0064/83 (GO-ESP)
T=0.0060/749 (TOPMED)
HGVS Names
  • CM000664.2:g.230178157C>T
  • NC_000002.11:g.231042873C>T
  • NC_000002.12:g.230178157C>T
  • NG_008295.1:g.46955G>A
  • NM_001185015.1:c.1465G>A
  • NM_004509.3:c.1447G>A
  • NM_004510.3:c.1447G>A
  • NM_080424.2:c.1447G>A
  • NP_001171944.1:p.Gly489Arg
  • NP_004500.3:p.Gly483Arg
  • NP_004501.3:p.Gly483Arg
  • NP_536349.2:p.Gly483Arg
  • XP_005246582.1:p.Gly489Arg
  • XP_005246583.1:p.Gly481Arg
  • XP_005246584.1:p.Gly280Arg
  • XP_006712550.1:p.Gly489Arg
  • XP_006712552.1:p.Gly489Arg
  • XP_011509390.1:p.Gly489Arg
  • XP_011509391.1:p.Gly483Arg
  • XP_011509392.1:p.Gly439Arg
  • XP_011509393.1:p.Gly489Arg
  • XP_011509394.1:p.Gly280Arg
  • XP_016859457.1:p.Gly489Arg
  • XP_016859458.1:p.Gly439Arg
  • XP_016859459.1:p.Gly433Arg
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 ss491262195 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs149485401 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
ss3303709101000GENOMES|20100804_snps_2014446_chr2_231042873fwd/C/Tttccaaagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaaatccc03/22/1103/22/11134Genomicunknown
ss342103035NHLBI-ESP|ESP2500-chr2-231042873byFreqfwd/BC/Tttccaaagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaaatccc03/25/1109/05/14134Genomicunknown
ss4898563101000GENOMES|20110521_exome_361499_chr2_231042873fwd/BC/Tttccaaagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaaatccc02/10/1202/21/12137Genomicunknown
ss491262195GSK-GENETICS|chr2_230751117fwd/BC/Tttccaaagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaaatccc03/02/1203/02/12137Genomicunknown
ss491332667EXOME_CHIP|splice_48894_chr_2_231042873fwd/BC/Tttccaaagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaaatccc03/05/1203/05/12137Genomicunknown
ss491801771CLINSEQ_SNP|SNV-chr2-230751117byFreqfwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa03/06/1209/05/14137Genomicunknown
ss534909392ILLUMINA|HumanOmni5-4v1_B_kgp24493988-0_T_R_1876436457fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa06/22/1208/28/15146Genomicunknown
ss780811433ILLUMINA|HumanOmni25Exome-8v1_A_exm273392-0_T_R_1918915780fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa05/30/1307/09/15146Genomicunknown
ss783493315ILLUMINA|HumanOmniExpressExome-8v1_A_exm273392-0_T_R_1918915780fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa05/31/1306/19/15146Genomicunknown
ss978060988EVA-GONL|EVA-GONL_rs149485401fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa04/23/1404/23/14142Genomicunknown
ss13020278681000GENOMES|PHASE3_V1_13213635fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa08/16/1408/16/14142Genomicunknown
ss1579363084EVA_GENOME_DK|EVA_GENOME_DK_snv_rs149485401fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa02/19/1502/20/15144Genomicunknown
ss1584024470EVA_FINRISK|EVA_FINRISK_rs149485401fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa02/27/1502/27/15144Genomicunknown
ss1587520777EVA_DECODE|EVA_DECODE_2_230751117_1722700_rs149485401fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa03/02/1503/03/15144Genomicunknown
ss1606002034EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_231042873_7281391fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa03/04/1503/04/15144Genomicunknown
ss1648996067EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_231042873_7281391fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa03/04/1503/04/15144Genomicunknown
ss1686776055EVA_EXAC|EVA_EXAC_1679661fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa03/04/1503/04/15144Genomicunknown
ss1710999570EVA_MGP|EVA_XIMO_116109fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa03/09/1503/09/15144Genomicunknown
ss1752343557ILLUMINA|OmniExpressExome-8v1-1_B_exm273392-0_T_R_1918915780fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa05/27/1506/09/15146Genomicunknown
ss1917761023ILLUMINA|HumanExome-12v1-1_B_exm273392-0_T_R_1918915780fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa10/16/1510/16/15147Genomicunknown
ss1946069055ILLUMINA|HumanCoreExome-12v1-0_C_exm273392-0_T_R_1918915780fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa10/29/1510/29/15147Genomicunknown
ss1958515616ILLUMINA|exm273392-0_T_R_1918915780fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa11/13/1511/13/15147Genomicunknown
ss2021202293JJLAB|SNP1704848fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa08/29/1608/30/16149Genomicunknown
ss2094915987ILLUMINA|Immuno_BeadChip_11419691_B_chr2_230751117-1_T_R_1770535398fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa09/27/1609/27/16150Genomicunknown
ss2095110440ILLUMINA|InfiniumImmunoArray-24v2-0_A_chr2_230751117-1_T_R_2310751271fwd/BC/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa09/27/1609/27/16150Genomicunknown
ss2239952854HUMAN_LONGEVITY|HLI-2-230178157-C-Tfwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa11/18/1611/18/16150Genomicunknown
ss2406409714TOPMED|2_231042873_C/Tfwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa11/19/1611/19/16150Genomicunknown
ss2733395272GNOMAD|exomes_rs149485401fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa05/17/1705/17/17151Genomicunknown
ss2746898452GNOMAD|coding_rs149485401fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa05/17/1705/17/17151Genomicunknown
ss2787407099GNOMAD|rs149485401fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa05/17/1705/17/17151Genomicunknown
ss2985202771AFFY|Axiom_PsorMich_Affx-52220034fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa05/24/1705/24/17151Genomicunknown
ss2991512426SWEGEN|NC_000002.11:g.231042873C>Tfwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa05/30/1705/30/17151Genomicunknown
ss3022080184ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm273392-0_T_R_1918915780fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa06/28/1706/28/17151Genomicunknown
ss3340886337TOPMED|TOPMed_freeze_5?chr2:230,178,157fwd/C/Taagagcagaagaccaaggaactcacgtgtttcattttcttcttatataaa10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs149485401|allelePos=252|totalLen=503|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 CCTACATGCA GCAAGGACAT GGCTGTCAGT ACAGCAGGGC CCATGGGTGA CTTCCAGGTG
 GGAGTGGAGG GTCTGATTGC CAGAAATACC ATGATGTGGA AGAGTTTGGA AATTCCTTCC
 TAAGAAGCGT TTCTTCTGCA GTCTAGCTAG CAGGGTCCAT TTCCTGATCA ATTACACACA
 CGGGTATTTT CCTCCCTTCT AGTGAGTCCT TCATCTAGGG ATTCCAAAGA GCAGAAGACC
 AAGGAACTCA C
 Y
 GTGTTTCATT TTCTTCTTAT ATAAAATCCC TTTCGCCTCA CCACAGGTCA CGGGGAGCTT
 AGAACAGTGA AAATCCACAG TGTCACTTTT GGGTTTTCCT TAAAGTAGAA GAGAACAGTT
 TTGTGTTATT CAGTCTTCAC TCCATCTTCC TTTTGAATTC TCCCCTCCAT GAATTCCAAT
 AATGTACAGG GTATTGGGGA ACGTTCTCTG GTTAGTTTGC AGGAACTCTT TCATCTCGAG
 TGACAGATAA G

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000002
dbSNP Blast Analysis
3D structure mapping
NP_001171944  NP_004500  NP_004501  NP_536349  

  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
ss1302027868EAS 1008AF 1.00000000
EUR 1006AF 0.981099960.01890000
AFR 1322AF 1.00000000
AMR 694AF 0.991400000.00860000
SAS 978AF 1.00000000
ss1686776055ExAc_Aggregated_Populations121406AF 0.992537440.00746256
ss342103035ESP_Cohort_Populations 4544GF0.985915480.01408451 0.751830000.992957770.00704225
ss491801771CSAgilent 1229GF0.983999970.01600000 1.000000000.991999980.00800000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.017+/-0.0920000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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