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Reference SNP (refSNP) Cluster Report: rs12722                 ** With Benign allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:52/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
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 Benign allele [ClinVar]
MAF/MinorAlleleCount:T=0.3494/1750 (1000 Genomes)
T=0.4136/51931 (TOPMED)
HGVS Names
  • CM000671.2:g.134842570C>T
  • NC_000009.11:g.137734416C>T
  • NC_000009.12:g.134842570C>T
  • NG_008030.1:g.205765C>T
  • NM_000093.4:c.*267C>T
  • NM_001278074.1:c.*267C>T
  • NR_103451.2:n.71-22361G>A
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 ss280430809 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12722 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
ss15014CGAP-GAI|59737fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc08/23/9910/10/0352cDNA99 %
ss1534855LEE|638777fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc09/13/0010/10/03100cDNAunknown
ss12941743SC_SNP|NT_019501.12_449881byFreqfwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc10/21/0305/16/04119Genomicunknown
ss16262246CGAP-GAI|1524664rev/TA/Ggctggaggcatggccccgctcccggggcgctgggtgtggacagagcgtggggcgggccca11/18/0311/22/03120cDNAunknown
ss24314771PERLEGEN|afd4274395byFreqfwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc08/10/0409/13/04123Genomicunknown
ss43910810ABI|hCV370252byFreqfwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc07/18/0511/03/06126Genomicunknown
ss76896408SI_EXO|NT_019501.13_643223byFreqfwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc09/20/0709/05/14129Genomicunknown
ss94189633BCMHGSC_JDW|JWB-2658979fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc02/26/0803/06/08129Genomicunknown
ss97836197HUMANGENOME_JCVI|1103652202306fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc03/30/0803/30/08130Genomicunknown
ss104660877BGI|BGI_rs12722fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc06/09/0806/18/09131Genomicunknown
ss133563214ENSEMBL|ENSSNP2946352fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc12/08/0810/15/09131Genomicunknown
ss144401562ENSEMBL|ENSSNP6151607fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc06/05/0906/06/09131Genomicunknown
ss160296974ILLUMINA|HumanOmni1-Quad_v1-0_B_rs12722-128_B_F_1562530530fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc08/04/0910/02/09131Genomicunknown
ss165028557COMPLETE_GENOMICS|NA07022_36_chr9_136874237fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc09/29/0909/30/09132Genomicunknown
ss167043026COMPLETE_GENOMICS|NA20431_36_chr9_136874237fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc09/30/0909/30/09132Genomicunknown
ss200986798BUSHMAN|BUSHMAN-chr9-136874236fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc02/16/1003/07/10132Genomicunknown
ss206867602BCM-HGSC-SUB|BCM_CMT_1011-1911261fwd/BC/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc03/15/1003/18/10132Genomicunknown
ss2244977891000GENOMES|pilot_1_YRI_6307472_chr9_136874237fwd/C/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc04/22/1004/22/10132Genomicunknown
ss2350022151000GENOMES|pilot_1_CEU_4606844_chr9_136874237fwd/C/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc05/01/1005/01/10132Genomicunknown
ss2417451491000GENOMES|pilot_1_CHB+JPT_3630226_chr9_136874237fwd/C/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc05/01/1005/01/10132Genomicunknown
ss280430809GMI|GMI_AK_SNP_4751126fwd/C/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc12/16/1012/16/10137Genomicunknown
ss286106604GMI|GMI_NA10851_SNP_2119385fwd/C/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc12/17/1012/17/10138Genomicunknown
ss294388129PJP|SNP_3894487_chr9_136874237fwd/C/Ttgggcccgccccacgctctgtccacacccagcgccccgggagcggggccatgcctccagc01/21/1101/21/11134Genomicunknown
ss480404668ILLUMINA|HumanOmni1-Quad_v1-0_C_rs12722-131_B_F_1863314977fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct01/30/1208/28/15146Genomicunknown
ss483810716ILLUMINA|HumanOmni2.5-4v1_D_kgp6906278-0_B_F_1801088868fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct01/30/1210/28/16137Genomicunknown
ss485745643ILLUMINA|HumanOmni2.5-4v1_B_SNP9-136874237-0_B_F_1612775973fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct01/30/1210/29/16137Genomicunknown
ss561689911TISHKOFF|snp_chr9_137734416fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct11/22/1211/23/12138Genomicunknown
ss656186328SSMP|9_137734416fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct12/14/1202/12/15138Genomicunknown
ss782348932ILLUMINA|HumanOmni2.5-4v1_H_kgp6906278-0_B_F_1801088868fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct05/30/1307/29/15146Genomicunknown
ss987067340EVA-GONL|EVA-GONL_rs12722fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct04/23/1404/25/14142Genomicunknown
ss1076669986JMKIDD_LAB|HGDP_WGS_chr9_137734416fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct07/10/1407/11/14142Genomicunknown
ss13357926101000GENOMES|PHASE3_V1_48377955fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct08/16/1408/16/14142Genomicunknown
ss1431985194DDI|DDI_rs12722fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct11/04/1411/05/14144Genomicunknown
ss1583290916EVA_GENOME_DK|EVA_GENOME_DK_snv_rs12722fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct02/19/1502/20/15144Genomicunknown
ss1596714614EVA_DECODE|EVA_DECODE_9_136874237_891247_rs12722fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct03/02/1503/03/15144Genomicunknown
ss1623741480EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_9_137734416_26745353fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct03/04/1503/04/15144Genomicunknown
ss1666735513EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_9_137734416_26745353fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct03/04/1503/04/15144Genomicunknown
ss1806200092HAMMER_LAB|Hsieh_5217359fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct07/15/1507/16/15146Genomicunknown
ss1930382374WEILL_CORNELL_DGM|SNV:chr9:137734416fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct10/16/1510/17/15147Genomicunknown
ss2025914706JJLAB|SNP6417261fwd/BC/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct08/29/1608/30/16149Genomicunknown
ss2154151206USC_VALOUEV|NC_000009.11:g.137734416C>Tfwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct11/17/1611/17/16150Genomicunknown
ss2315133214HUMAN_LONGEVITY|HLI-9-134842570-C-Tfwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct11/18/1611/18/16150Genomicunknown
ss2485665464TOPMED|9_137734416_C/Tfwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct11/20/1611/20/16150Genomicunknown
ss2627425345SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV4071601fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct01/06/1701/06/17151Genomicunknown
ss2634928557ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp6906278-0_B_F_180108886fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct02/02/1702/02/17151Genomicunknown
ss2710036597GRF|rs12722fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct02/13/1702/13/17151Genomicunknown
ss2884169030GNOMAD|rs12722fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct05/19/1705/19/17151Genomicunknown
ss3005731815SWEGEN|NC_000009.11:g.137734416C>Tfwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct05/30/1705/30/17151Genomicunknown
ss3022975583ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs12722-138_B_F_2258077686fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct06/28/1706/28/17151Genomicunknown
ss3022975584ILLUMINA|MEGA_Consortium_v2_15070954_A2_seq2_rs12722_fwd-138_B_F_23149798fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct06/28/1706/28/17151Genomicunknown
ss3022975585ILLUMINA|MEGA_Consortium_v2_15070954_A2_seq2_rs12722_rev-138_T_R_23149798fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct06/28/1706/28/17151Genomicunknown
ss3022975586ILLUMINA|MEGA_Consortium_v2_15070954_A2_seq3_rs12722_fwd-138_B_F_23149798fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct06/28/1706/28/17151Genomicunknown
ss3022975587ILLUMINA|MEGA_Consortium_v2_15070954_A2_seq_rs12722_fwd-138_B_F_231497981fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct06/28/1706/28/17151Genomicunknown
ss3026739637BIOINF_KMB_FNS_UNIBA|9.134842570C>Tfwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct07/05/1707/05/17151Genomicunknown
ss3348896655CSHL|rs12722fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct10/02/1710/02/17151Genomicunknown
ss3602770642TOPMED|TOPMed_freeze_5?chr9:134,842,570fwd/C/Tccgccccacgctctgtccacacccagcgccccgggagcggggccatgcct10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12722|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 AGCCAGACAG ATTGTGGGGG GTGATTGGTA AACCCCAAGA CCCCCAACTG TTCTTAACCA
 CCGGCCATCT GTCTCCCTCT TCCCCAGACC AAGAAAGGCT ACCAGAAGAC GGTTCTGGAG
 ATCGACACCC CCAAAGTGGA GCAGGTGCCC ATCGTGGACA TCATGTTCAA TGACTTCGGT
 GAAGCGTCAC AGAAATTTGG ATTTGAAGTG GGGCCGGCTT GCTTCATGGG CTAGGAGCCG
 CCGAGCCCGG GCTCCCGAGA GCAACCTCGT GACCTCAGCA TGCCATTCGT TCGTGAGTGT
 CCCGTGCACG TCCTGACCCT GGACAGTGAA GGCTTCTCCC TCCCCTCCCA CCTGACTTCA
 TCTACGCCTC GGCACCACGG GGTGTGGGAC CCCAGCCCGG AGAGAACAGA GGGAAGGAGC
 CGCGCCCCCA CCTGGAGCTG AATCACATGA CCTAGCTGCA CCCCAGCGCC TGGGCCCGCC
 CCACGCTCTG TCCACACCCA
 Y
 GCGCCCCGGG AGCGGGGCCA TGCCTCCAGC CCCCCAGCTC GCCCGACCCA TCCTGTTCGT
 GAATAGGTCT CAGGGGTTGG GGGAGGGACT GCCAGATTTG GACACTATAT TTTTTTCTAA
 ATTCAACTTG AAGATGTGTA TTTCCCCTGA CCTTCAAAAA ATGTTCCAAG GTAAGCCTCG
 TAAAGGTCAT CCCACCATCA CCAAAGCCTC CGTTTTTAAC AACCTCCAAC ACGATCCATT
 TAGAGGCCAA ATGTCATTCT GCAGGTGCCT TCCCGATGGA TTAAAGGTGC TTATGTTTTT
 GTGAGTTTTA AGTAAATATT TGTATTGTAT TGTTATAAAT GTTAAGTGTG CCTGGCTTTC
 AATCATGCAC GGAAACCCAG TCTCAGTCCC ACGGACAGAA TGGGCGAGGC ATGGATTCTG
 GGTTGCAGTA CCGTTCTGAT TAGAAATAGG AAGTCTCCCC ACCCCCGCCC TGGCCAAGAA
 CGTGCAATAA ATTGGAAGTT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_019501.13 ABBA01030015 AW007298 Hs.146428 M76729
dbSNP Blast Analysis
UniGene Cluster ID
210283

  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
ss12941743CEPH 184AF 0.560000000.44000000
ss133563214ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss1335792610EAS 1008AF 0.779800000.22019999
EUR 1006AF 0.414500000.58550000
AFR 1322AF 0.854800050.14520000
AMR 694AF 0.554799970.44520003
SAS 978AF 0.552100000.44790000
ss144401562ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss165028557CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss167043026PGP 2IG 1.00000000 0.500000000.50000000
ss200986798BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss224497789pilot_1_YRI_low_coverage_panel 118AF 0.915254240.08474576
ss235002215pilot_1_CEU_low_coverage_panel 120AF 0.441666660.55833334
ss241745149pilot_1_CHB+JPT_low_coverage_panel 120AF 0.800000010.20000000
ss24314771AFD_EUR_PANELEuropean 40IG0.200000000.300000010.500000000.150222000.349999990.64999998
AFD_AFR_PANELAfrican American 46IG0.565217380.391304340.043478260.751830000.760869560.23913044
AFD_CHN_PANELAsian 42IG0.666666690.33333334 0.654721000.833333310.16666667
ss76896408HapMap-CEUEuropean 106IG0.113207550.641509410.245283020.050043000.433962260.56603771
HapMap-HCBAsian 86IG0.604651150.348837200.046511631.000000000.779069780.22093023
HapMap-JPTAsian 82IG0.707317050.268292700.024390241.000000000.841463390.15853658
HapMap-YRISub-Saharan African 118IG0.728813590.27118644 0.583882000.864406760.13559322
ss97836197J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.455+/-0.1440000

  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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