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Reference SNP (refSNP) Cluster Report: rs3750430                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/T (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.1474/738 (1000 Genomes)
T=0.0832/10441 (TOPMED)
HGVS Names
  • CM000671.2:g.35658166A>C
  • CM000671.2:g.35658166A>T
  • NC_000009.11:g.35658163A>T
  • NC_000009.12:g.35658166A>C
  • NC_000009.12:g.35658166A>T
  • NG_017041.1:g.4853T>A
  • NG_017041.1:g.4853T>G
  • NG_033120.1:g.4877A>C
  • NG_033120.1:g.4877A>T
  • NM_001195200.1:c.-214A>C
  • NM_001195200.1:c.-214A>T
  • NM_001195201.1:c.-214A>C
  • NM_001195201.1:c.-214A>T
  • NM_001195217.1:c.-214A>C
  • NM_001195217.1:c.-214A>T
  • NM_174923.2:c.-214A>C
  • NM_174923.2:c.-214A>T
  • NR_003051.3:n.-148T>A
  • NR_003051.3:n.-148T>G
  • XR_242498.1:n.-116A>T
  • XR_929218.2:n.-116A>C
  • XR_929218.2:n.-116A>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 ss280194080 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3750430 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
ss4936456YUSUKE|IMS-JST102366byFreqfwd/TA/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca08/01/0210/10/03107Genomicunknown
ss6742741WI_SSAHASNP|NT_023974.13_8612100fwd/TA/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca02/12/0310/25/06111Genomicunknown
ss20365350CSHL-HAPMAP|CSHL-HuFF-200402.chr9.NT_008413.16_35648163fwd/TA/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca02/21/0403/04/04120Genomicunknown
ss43873154ABI|hCV27494993byFreqfwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca07/18/0511/03/06126Genomicunknown
ss69289504PERLEGEN|PGP04395731byFreqfwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca01/30/0703/31/08127Genomicunknown
ss94048118BCMHGSC_JDW|JWB-2588141fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca02/26/0803/05/08129Genomicunknown
ss104615145BGI|BGI_rs3750430fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca06/08/0806/18/09131Genomicunknown
ss144088312ENSEMBL|ENSSNP13637085fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca06/05/0906/06/09131Genomicunknown
ss157434116GMI|GMI_SNP_69424114fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca06/24/0906/25/09131Genomicunknown
ss160636269ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3750430-128_T_F_1578101168fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca08/04/0910/04/09131Genomicunknown
ss161720128ENSEMBL|ENSSNP2987025byFreqfwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca09/24/0903/07/10131Genomicunknown
ss2107609251000GENOMES|YRI.trio.3.2010_879209_chr9_35648163fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca03/29/1003/29/10132Genomicunknown
ss2242313001000GENOMES|pilot_1_YRI_6040983_chr9_35648163fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca04/22/1004/22/10132Genomicunknown
ss2348061431000GENOMES|pilot_1_CEU_4410772_chr9_35648163fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca05/01/1005/01/10132Genomicunknown
ss2415846401000GENOMES|pilot_1_CHB+JPT_3469717_chr9_35648163fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca05/01/1005/01/10132Genomicunknown
ss280194080GMI|GMI_AK_SNP_4514353fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca12/16/1012/16/10137Genomicunknown
ss294439353PJP|SNP_3945711_chr9_35648163fwd/A/Tagactataggctttcagaggcattgtggctgcagaatagctaatagacacgaaatgaaca01/21/1101/21/11134Genomicunknown
ss481759864ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3750430-131_T_F_1863364244fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat01/30/1208/28/15146Genomicunknown
ss561368078TISHKOFF|snp_chr9_35658163fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat11/22/1211/23/12138Genomicunknown
ss655812376SSMP|9_35658163fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat12/14/1202/12/15138Genomicunknown
ss986526501EVA-GONL|EVA-GONL_rs3750430fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat04/23/1404/25/14142Genomicunknown
ss1076281403JMKIDD_LAB|HGDP_WGS_chr9_35658163fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat07/10/1407/11/14142Genomicunknown
ss13337213561000GENOMES|PHASE3_V1_46219482fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat08/16/1408/16/14142Genomicunknown
ss1583074997EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3750430fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat02/19/1502/20/15144Genomicunknown
ss1596164705EVA_DECODE|EVA_DECODE_9_35648163_341326_rs3750430fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat03/02/1503/03/15144Genomicunknown
ss1622678931EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_9_35658163_25573529fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat03/04/1503/04/15144Genomicunknown
ss1665672964EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_9_35658163_25573529fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat03/04/1503/04/15144Genomicunknown
ss1929811752WEILL_CORNELL_DGM|SNV:chr9:35658163fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat10/16/1510/17/15147Genomicunknown
ss1959180773ILLUMINA|rs3750430-138_T_F_2289614698fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat11/13/1511/13/15147Genomicunknown
ss2025619450JJLAB|SNP6122005fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat08/29/1608/30/16149Genomicunknown
ss2153847164USC_VALOUEV|NC_000009.11:g.35658163A>Tfwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat11/17/1611/17/16150Genomicunknown
ss2311071248HUMAN_LONGEVITY|HLI-9-35658166-A-Tfwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat11/18/1611/18/16150Genomicunknown
ss2481209725TOPMED|9_35658163_A/Tfwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat11/20/1611/20/16150Genomicunknown
ss2627284349SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV3892807fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat01/06/1701/06/17151Genomicunknown
ss2709657546GRF|rs3750430fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat02/13/1702/13/17151Genomicunknown
ss2711162258ILLUMINA|Consortium-OncoArray_15047405_A_chr9_35658163_A_T-100_T_F_219903fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat03/22/1703/22/17151Genomicunknown
ss2877732854GNOMAD|rs3750430fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat05/19/1705/19/17151Genomicunknown
ss2986106374AFFY|Axiom_Smokesc1_Affx-33717218fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat05/24/1705/24/17151Genomicunknown
ss3004710800SWEGEN|NC_000009.11:g.35658163A>Tfwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat05/30/1705/30/17151Genomicunknown
ss3022925719ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs3750430-138_T_F_2289614698fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat06/28/1706/28/17151Genomicunknown
ss3026599828BIOINF_KMB_FNS_UNIBA|9.35658166A>Tfwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat07/05/1707/05/17151Genomicunknown
ss3348621318CSHL|rs3750430fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat10/02/1710/02/17151Genomicunknown
ss3587357632TOPMED|TOPMed_freeze_5?chr9:35,658,166-01fwd/A/Cataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat10/07/1710/07/17151Genomicunknown
ss3587357633TOPMED|TOPMed_freeze_5?chr9:35,658,166-02fwd/A/Tataggctttcagaggcattgtggctgcagaatagctaatagacacgaaat10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3750430|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/T'|mol=Genomic|build=151
 CCAACTACTT GGGAGCCTGA GGTGAGGCAT CGCGTGAGCC CGGGGAGGTC GAGGCTGCAG
 TGAGCCGTGG TCTCGGGAAC AAAAAACAGC CGCGCTGAGA ATGAGCCCCG TGTGGTTGGT
 GCGCGGACAC GCACTGCCTG CGTAACTAGA GGGAGCTGAC GGATGACGCC CCCGCGCCAC
 GCCGCTCAGC GGGATACGCT TCTTGGCGGA CTTTGGAGTG GGAAGCGGGG AATGTCTACG
 TGCGTATGCA CGTGGCACTC TCTGCCCGAG GTCCGGGGAC TTTCCCCTAG GCGGAAAGGG
 GAGGAACAGA GTCCTCAGTG TGTAGCCTAG GATACAGGCC TTCAGCACGA ACCACGTCCT
 CAGCTTCACA GAGTAGTATT TTATAGCCCT AAAGAAATTG TGTTTTATGA TTAGGGTGAG
 AAAGTTGGTG GCGTGAGATT AAAAAAACCG TTTTCGGGCA TAACTTTCTA AGACTATAGG
 CTTTCAGAGG CATTGTGGCT
 H
 GCAGAATAGC TAATAGACAC GAAATGAACA AATACAGGAA AGCTAGAATG ACACTATCTT
 ATGCAAATAT GGTCTGGCCC CGCCCTACGG GGAGTGGGCG TGGCCTCCCC GGAGCCGGCC
 GGCCTGCTCG CGTGCGCGTG CGCGTTGGGG CGGCCGGCCA ATGCCGGACC GCTTCGGCAC
 CGCCCGCCCG ATCCCTCCAC CCGTGGGCCG GCAATGGCGG GCGCAGTTTC GCTCTTGGGT
 GTGGTGGGGC TGCTGCTTGT GTCTGCGCTG TCCGGGGTCC TAGGAGACCG CGCCAATCCC
 GACCTCCGGG CACACCCAGG TACCAGCTAG GGCTGCTGGA GGAGGGCTGG GACTGCGCAC
 GGGTCCCAGG CCCCAGCTCG GCTGACTCGC CTGTATCCTC CCTCCGCAGG GAACGCAGCC
 CACCCCGGCT CTGGAGCCAC GGAACCCCGG CGGCGACCAC CGCTCAAGGA TCAACGCGAG
 CGGACCCGGG CCGGGTCGCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_023942.1
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.
SourceA/A
A/T
T/T
HWPA
T
ss1333721356EAS 1008AF 0.668700040.33130002
EUR 1006AF 0.927399990.07260000
AFR 1322AF 0.953099970.04690000
AMR 694AF 0.850100040.14990000
SAS 978AF 0.831300020.16869999
ss144088312ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss161720128ENSEMBL_celera 4IG0.50000000 0.50000000 0.500000000.50000000
ss224231300pilot_1_YRI_low_coverage_panel 118AF 0.923728820.07627118
ss234806143pilot_1_CEU_low_coverage_panel 120AF 0.958333310.04166667
ss241584640pilot_1_CHB+JPT_low_coverage_panel 120AF 0.649999980.34999999
ss43873154HapMap-CEUEuropean 120IG0.899999980.10000000 1.000000000.949999990.05000000
HapMap-HCBAsian 90IG0.488888890.466666670.044444450.294266000.722222210.27777779
HapMap-JPTAsian 88IG0.318181810.545454560.136363640.402784000.590909060.40909091
HapMap-YRISub-Saharan African 120IG0.899999980.083333340.016666670.099721000.941666660.05833333
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss4936456JBIC-allele 1466AF 0.592800020.40720001
ss69289504HapMap-CEUEuropean 120IG0.899999980.10000000 1.000000000.949999990.05000000
HapMap-HCBAsian 90IG0.488888890.422222230.088888891.000000000.699999990.30000001
HapMap-JPTAsian 90IG0.311111120.511111140.177777781.000000000.566666660.43333334
HapMap-YRISub-Saharan African 120IG0.899999980.083333340.016666670.099721000.941666660.05833333

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.251+/-0.2500000

  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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