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Reference SNP (refSNP) Cluster Report: rs3196378                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:105/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
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:With Benign allele [ClinVar]
MAF/MinorAlleleCount:A=0.3253/1629 (1000 Genomes)
A=0.3964/49779 (TOPMED)
HGVS Names
  • CM000671.2:g.134843036C>A
  • CM000671.2:g.134843036C>G
  • CM000671.2:g.134843036C>T
  • NC_000009.11:g.137734882C>A
  • NC_000009.11:g.137734882C>G
  • NC_000009.11:g.137734882C>T
  • NC_000009.12:g.134843036C>A
  • NC_000009.12:g.134843036C>G
  • NC_000009.12:g.134843036C>T
  • NG_008030.1:g.206231C>A
  • NG_008030.1:g.206231C>G
  • NG_008030.1:g.206231C>T
  • NM_000093.4:c.*733C>A
  • NM_000093.4:c.*733C>G
  • NM_000093.4:c.*733C>T
  • NM_001278074.1:c.*733C>A
  • NM_001278074.1:c.*733C>G
  • NM_001278074.1:c.*733C>T
  • NR_103451.2:n.71-22827G>A
  • NR_103451.2:n.71-22827G>C
  • NR_103451.2:n.71-22827G>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 ss280430811 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3196378 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
ss4423565LEE|e641497fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga04/26/0210/10/03105cDNAunknown
ss15859832SC_SNP|NT_019501.12_450347byFreqfwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga11/17/0305/16/04120Genomicunknown
ss43804118ABI|hCV370253fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga07/18/0507/18/05126Genomicunknown
ss71643367SI_EXO|NT_019501.13_643689fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga05/07/0705/07/07127Genomicunknown
ss94189636BCMHGSC_JDW|JWB-2658980fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga02/26/0803/06/08129Genomicunknown
ss104660878BGI|BGI_rs3196378fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga06/09/0806/18/09131Genomicunknown
ss104801171KRIBB_YJKIM|KHS1106216fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga06/09/0806/09/08130Genomicunknown
ss1091277671000GENOMES|CEU.trio.12.15.2008_2268506_chr9_136874703fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga12/16/0812/16/08130Genomicunknown
ss144401566ENSEMBL|ENSSNP13732298fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga06/05/0906/06/09131Genomicunknown
ss160615734ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3196378-128_T_F_1562530535fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga08/04/0910/04/09131Genomicunknown
ss165028570COMPLETE_GENOMICS|NA07022_36_chr9_136874703fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga09/29/0909/30/09132Genomicunknown
ss167043035COMPLETE_GENOMICS|NA20431_36_chr9_136874703fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga09/30/0909/30/09132Genomicunknown
ss200986806BUSHMAN|BUSHMAN-chr9-136874702fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga02/16/1003/07/10132Genomicunknown
ss206760900BCM-HGSC-SUB|BCM_CMT_1011-1872385fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga03/15/1003/18/10132Genomicunknown
ss2244977941000GENOMES|pilot_1_YRI_6307477_chr9_136874703fwd/A/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga04/22/1004/22/10132Genomicunknown
ss2350022181000GENOMES|pilot_1_CEU_4606847_chr9_136874703fwd/A/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga05/01/1005/01/10132Genomicunknown
ss2417451511000GENOMES|pilot_1_CHB+JPT_3630228_chr9_136874703fwd/A/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga05/01/1005/01/10132Genomicunknown
ss254624986BL|SNP129085_9_136874703fwd/TA/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga08/19/1008/19/10134Genomicunknown
ss280430811GMI|GMI_AK_SNP_4751128fwd/A/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga12/16/1012/16/10137Genomicunknown
ss286106605GMI|GMI_NA10851_SNP_2119386fwd/A/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga12/17/1012/17/10138Genomicunknown
ss294388130PJP|SNP_3894488_chr9_136874703fwd/A/Cctgattagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaattgga01/21/1101/21/11134Genomicunknown
ss481677379ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3196378-131_T_F_1863370065fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa01/30/1208/28/15146Genomicunknown
ss483196182ILLUMINA|HumanOmni2.5-4v1_D_kgp3571189-0_B_R_1800966508fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa01/30/1210/28/16137Genomicunknown
ss485745649ILLUMINA|HumanOmni2.5-4v1_B_SNP9-136874703-0_B_R_1634604743fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa01/30/1210/29/16137Genomicunknown
ss535416289ILLUMINA|HumanOmni5-4v1_B_kgp3571189-0_B_R_1800966508fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa06/22/1208/29/15146Genomicunknown
ss561689915TISHKOFF|snp_chr9_137734882fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa11/22/1211/23/12138Genomicunknown
ss656186333SSMP|9_137734882fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa12/14/1202/12/15138Genomicunknown
ss779500333ILLUMINA|HumanOmni25Exome-8v1_A_kgp3571189-0_B_R_1800966508fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa05/30/1307/10/15146Genomicunknown
ss782041357ILLUMINA|HumanOmni2.5-4v1_H_kgp3571189-0_B_R_1800966508fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa05/30/1307/29/15146Genomicunknown
ss834970561ILLUMINA|HumanOmni2.5-8v1_A_kgp3571189-0_B_R_1800966508fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa09/18/1307/29/15146Genomicunknown
ss987067347EVA-GONL|EVA-GONL_rs3196378fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa04/23/1404/25/14142Genomicunknown
ss1076669990JMKIDD_LAB|HGDP_WGS_chr9_137734882fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa07/10/1407/11/14142Genomicunknown
ss13357926311000GENOMES|PHASE3_V1_48377977fwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa08/16/1408/16/14142Genomicunknown
ss1431985196DDI|DDI_rs3196378fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa11/04/1411/05/14144Genomicunknown
ss1583290920EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3196378fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa02/19/1502/20/15144Genomicunknown
ss1623741494EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_9_137734882_26745367fwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa03/04/1503/04/15144Genomicunknown
ss1666735527EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_9_137734882_26745367fwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa03/04/1503/04/15144Genomicunknown
ss1711242408EVA_MGP|EVA_XIMO_358168fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa03/09/1503/09/15144Genomicunknown
ss1930382383WEILL_CORNELL_DGM|SNV:chr9:137734882fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa10/16/1510/17/15147Genomicunknown
ss1971325331GENOMED|rs3196378fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa02/16/1602/16/16147Genomicunknown
ss2025914711JJLAB|SNP6417266fwd/TA/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa08/29/1608/30/16149Genomicunknown
ss2154151209USC_VALOUEV|NC_000009.11:g.137734882C>Afwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa11/17/1611/17/16150Genomicunknown
ss2315133251HUMAN_LONGEVITY|HLI-9-134843036-C-A,G,Tfwd/A/C/G/Ttagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa11/18/1611/18/16150Genomicunknown
ss2485665499TOPMED|9_137734882_C/Afwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa11/20/1611/20/16150Genomicunknown
ss2627425346SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV4071602fwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa01/06/1701/06/17151Genomicunknown
ss2634928560ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp3571189-0_B_R_180096650fwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa02/02/1702/02/17151Genomicunknown
ss2710036601GRF|rs3196378fwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa02/13/1702/13/17151Genomicunknown
ss2884169080GNOMAD|rs3196378fwd/A/C/Ttagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa05/19/1705/19/17151Genomicunknown
ss3005731827SWEGEN|NC_000009.11:g.137734882C>Afwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa05/30/1705/30/17151Genomicunknown
ss3026739638BIOINF_KMB_FNS_UNIBA|9.134843036C>Afwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa07/05/1707/05/17151Genomicunknown
ss3348896657CSHL|rs3196378fwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa10/02/1710/02/17151Genomicunknown
ss3602770744TOPMED|TOPMed_freeze_5?chr9:134,843,036-01fwd/A/Ctagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa10/07/1710/07/17151Genomicunknown
ss3602770745TOPMED|TOPMed_freeze_5?chr9:134,843,036-02fwd/C/Gtagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa10/07/1710/07/17151Genomicunknown
ss3602770746TOPMED|TOPMed_freeze_5?chr9:134,843,036-03fwd/C/Ttagaaataggaagtctccccaccccgccctggccaagaacgtgcaataaa10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3196378|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/G/T'|mol=Genomic|build=151
 CGCCTGGGCC CGCCCCACGC TCTGTCCACA CCCACGCGCC CCGGGAGCGG GGCCATGCCT
 CCAGCCCCCC AGCTCGCCCG ACCCATCCTG TTCGTGAATA GGTCTCAGGG GTTGGGGGAG
 GGACTGCCAG ATTTGGACAC TATATTTTTT TCTAAATTCA ACTTGAAGAT GTGTATTTCC
 CCTGACCTTC AAAAAATGTT CCAAGGTAAG CCTCGTAAAG GTCATCCCAC CATCACCAAA
 GCCTCCGTTT TTAACAACCT CCAACACGAT CCATTTAGAG GCCAAATGTC ATTCTGCAGG
 TGCCTTCCCG ATGGATTAAA GGTGCTTATG TTTTTGTGAG TTTTAAGTAA ATATTTGTAT
 TGTATTGTTA TAAATGTTAA GTGTGCCTGG CTTTCAATCA TGCACGGAAA CCCAGTCTCA
 GTCCCACGGA CAGAATGGGC GAGGCATGGA TTCTGGGTTG CAGTACCGTT CTGATTAGAA
 ATAGGAAGTC TCCCCACCCC
 N
 GCCCTGGCCA AGAACGTGCA ATAAATTGGA AGTTTGCCCC GGGGCAGCAA GAATTTATGC
 TGCCATTGAA AAGCAGGTAC CAGTGCCCCT TTTCAGACAG TTTTTGATTC GCTCTAGACT
 TTTTTTTTTT TTAATAGGGA AAAAATTTGA TAATTTTCTT TTTTCTACAT GCACTTAAGA
 CTAAAACACA GGTTTGGATT AATTTTATTT GCTTCCTTTT TCCGCTTTTC TTCCCGCAGA
 GCCTGATGGG AGAATGTCCA GGGCAGGGAA ACCACATTTT TTGTAGGTGA TAACTCAATG
 AAAATTGGTG CTTATTTTTT ACACTTCTCT CTTGTGGCTC TCTTGTGGTG CTATCTATCT
 GTTTTAAGGT CTCCTTGAAG GCGCACTGGG GACCCTGGCC ATGCCTCGTT CTCCCTGCTT
 TCTTTATCCT GTTATTGCCT CCACAGTCTG TTGCCAAGGA CTCTAAGATC AATGCACGTC
 ACTTTCCTTT CCACTGGGCA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_019501.13 Hs.146428
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/C
HWPA
C
ss1335792631EAS 1008AF 0.223199990.77679998
EUR 1006AF 0.581499990.41849998
AFR 1322AF 0.112000000.88800001
AMR 694AF 0.437999960.56200004
SAS 978AF 0.375299990.62470001
ss144401566ENSEMBL_Watson 2IG1.00000000 0.500000000.50000000
ss15859832CEPH 184AF 0.519999980.47999999
ss165028570CEUEuropean 2IG1.00000000 0.500000000.50000000
ss167043035PGP 2IG1.00000000 0.500000000.50000000
ss200986806BUSHMAN_POP2 2IG1.00000000 0.500000000.50000000
ss224497794pilot_1_YRI_low_coverage_panel 118AF 0.084745760.91525424
ss235002218pilot_1_CEU_low_coverage_panel 120AF 0.616666670.38333333
ss241745151pilot_1_CHB+JPT_low_coverage_panel 120AF 0.200000000.80000001

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.439+/-0.1640000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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