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Reference SNP (refSNP) Cluster Report: rs12896790                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:121/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:G/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.0840/10187 (ExAC)
G=0.0507/254 (1000 Genomes)
G=0.0744/967 (GO-ESP)
G=0.0608/7640 (TOPMED)
HGVS Names
  • CM000676.2:g.37804717T>G
  • NC_000014.8:g.38273922T>G
  • NC_000014.9:g.37804717T>G
  • NM_001310135.1:c.4115T>G
  • NP_001297064.1:p.Ile1372Ser
  • XP_003960024.2:p.Ile420Ser
  • XP_011535732.1:p.Ile891Ser
  • XP_011535733.1:p.Ile785Ser
  • XP_016876743.1:p.Ile1372Ser
  • XP_016876745.1:p.Ile1039Ser
  • XR_943762.1:n.4972T>G
Links , Linkout
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 ss43583213 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12896790 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
ss21223577SSAHASNP|WGSA-200403-chr14.chr14.NT_026437.10_18193961fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac03/19/0403/19/04121Genomicunknown
ss43583213ABI|hCV3059960byFreqfwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac07/18/0511/03/06126Genomicunknown
ss66702470ILLUMINA|HumanHap300v1.1_rs12896790fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac11/09/0611/09/06127Genomicunknown
ss67044871ILLUMINA|HumanHap550v1.1_rs12896790fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac11/14/0611/14/06127Genomicunknown
ss67370106ILLUMINA|HumanHap650Yv1.0_rs12896790fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac11/14/0611/14/06127Genomicunknown
ss69154466PERLEGEN|PGP08064197byFreqfwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac01/30/0703/31/08127Genomicunknown
ss70417135ILLUMINA|HumanHap300v2.0_rs12896790fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac04/18/0711/18/07127Genomicunknown
ss70587669ILLUMINA|HumanHap550v3.0__rs12896790rev/TA/Cgtggcatctggtcctttatcagaatgagaatggcatccaaagccttcttaagcacttcca04/20/0703/30/08130Genomicunknown
ss71130841ILLUMINA|HumanHap650Yv3.0_rs12896790fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac04/23/0704/23/07127Genomicunknown
ss74819429AFFY|SNP_M-320292fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac08/09/0708/09/07128Genomicunknown
ss75656425ILLUMINA|ILMN_Human_1M_rs12896790fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac08/28/0708/29/07129Genomicunknown
ss76662618AFFY|AFFY_6_1M_SNP_A-8523828rev/TA/Ctttatcagaatgagaatggcatccaaagcctt08/28/0708/30/07129Genomicunknown
ss85281222KRIBB_YJKIM|KHS948969fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac12/04/0712/08/07130Genomicunknown
ss96908972HUMANGENOME_JCVI|1103649036859fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac03/27/0803/27/08130Genomicunknown
ss121608261ILLUMINA|HumanCNV370v1_C_rs12896790fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac04/14/0904/14/09131Genomicunknown
ss137064646ENSEMBL|ENSSNP986820fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac12/08/0810/15/09131Genomicunknown
ss153291971ILLUMINA|Human610_Quadv1_B_rs12896790-127_T_R_1501648773rev/TA/Cgtggcatctggtcctttatcagaatgagaatggcatccaaagccttcttaagcacttcca06/18/0906/19/09131Genomicunknown
ss159237879ILLUMINA|Human660W-Quad_v1_A_rs12896790-128_T_R_1501648773rev/TA/Cgtggcatctggtcctttatcagaatgagaatggcatccaaagccttcttaagcacttcca07/06/0907/06/09131Genomicunknown
ss159729111SEATTLESEQ|TTC6-37343673fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac07/10/0907/10/09131Genomicunknown
ss160305150ILLUMINA|HumanOmni1-Quad_v1-0_B_rs12896790-128_T_R_1512016707rev/TA/Cgtggcatctggtcctttatcagaatgagaatggcatccaaagccttcttaagcacttcca08/04/0910/02/09131Genomicunknown
ss170249581ILLUMINA|HumanCNV370-Quadv3_C_rs12896790-127_T_R_1501648773rev/TA/Cgtggcatctggtcctttatcagaatgagaatggcatccaaagccttcttaagcacttcca10/01/0910/03/09132Genomicunknown
ss172269891ILLUMINA|Human1M-Duov3_B_rs12896790-127_T_R_1501648773rev/TA/Cgtggcatctggtcctttatcagaatgagaatggcatccaaagccttcttaagcacttcca10/01/0910/02/09132Genomicunknown
ss2365007911000GENOMES|pilot_1_CEU_6105420_chr14_37343673fwd/G/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac05/01/1005/01/10132Genomicunknown
ss254914008BL|SNP22083_14_37343673fwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac08/19/1008/19/10134Genomicunknown
ss291703410PJP|SNP_1209768_chr14_37343673fwd/G/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac01/21/1101/21/11134Genomicunknown
ss342385839NHLBI-ESP|ESP2500-chr14-38273922byFreqfwd/BG/Ttggaagtgcttaagaaggctttggatgccattctcattctgataaaggaccagatgccac03/25/1109/05/14134Genomicunknown
ss479836422ILLUMINA|HumanOmni2.5-4v1_B_rs12896790-128_T_R_1735634806fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat01/30/1210/28/16137Genomicunknown
ss479843798ILLUMINA|HumanOmniExpress-12v1_C_rs12896790-131_T_R_1857492233fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat01/30/1210/27/16137Genomicunknown
ss480437353ILLUMINA|HumanOmni1-Quad_v1-0_C_rs12896790-131_T_R_1865615283fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat01/30/1208/28/15146Genomicunknown
ss484716664ILLUMINA|HumanOmni2.5-4v1_D_rs12896790-131_T_R_1857492233fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat01/30/1210/27/16137Genomicunknown
ss491686562CLINSEQ_SNP|SNV-chr14-37343673byFreqfwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat03/06/1209/05/14137Genomicunknown
ss536819997ILLUMINA|HumanOmni5-4v1_B_rs12896790-131_T_R_1866534261fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat06/22/1208/29/15146Genomicunknown
ss659696873SSMP|14_38273922fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat12/14/1202/13/15138Genomicunknown
ss778417392ILLUMINA|HumanOmni25Exome-8v1_A_rs12896790-131_T_R_1866534261fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat05/30/1307/10/15146Genomicunknown
ss782805070ILLUMINA|HumanOmni2.5-4v1_H_rs12896790-131_T_R_1857492233fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat05/30/1307/29/15146Genomicunknown
ss783770471ILLUMINA|HumanOmniExpressExome-8v1_A_rs12896790-131_T_R_1967886659fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat05/31/1306/18/15146Genomicunknown
ss825386409ILLUMINA|HumanCNV370v1_C_rs12896790-126_T_R_IFB1135963058:0fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat06/24/1311/21/14144Genomicunknown
ss832058159ILLUMINA|HumanOmniExpress-12v1_H_rs12896790-131_T_R_1857492233fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat09/17/1306/18/15146Genomicunknown
ss833872730ILLUMINA|HumanOmni2.5-8v1_A_rs12896790-131_T_R_1866534261fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat09/18/1307/29/15146Genomicunknown
ss974488373JMKIDD_LAB|KhoeSan_Exomes_chr14_38273922fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat03/06/1403/06/14142Genomicunknown
ss991035358EVA-GONL|EVA-GONL_rs12896790fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat04/23/1404/25/14142Genomicunknown
ss1067545120JMKIDD_LAB|HGDP_exomes_chr14_38273922fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat07/09/1407/09/14142Genomicunknown
ss1079569713JMKIDD_LAB|HGDP_WGS_chr14_38273922fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat07/10/1407/12/14142Genomicunknown
ss13505930771000GENOMES|PHASE3_V1_63802047fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat08/16/1408/16/14142Genomicunknown
ss1397677647HAMMER_LAB|HAMMER_LAB_rs12896790fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat09/30/1409/30/14146Genomicunknown
ss1427390611DDI|DDI_rs12896790fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat11/04/1411/04/14144Genomicunknown
ss1577181418EVA_GENOME_DK|EVA_GENOME_DK_snv_rs12896790fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat02/19/1502/19/15144Genomicunknown
ss1584089422EVA_FINRISK|EVA_FINRISK_rs12896790fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat02/27/1502/27/15144Genomicunknown
ss1691457952EVA_EXAC|EVA_EXAC_6730108fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat03/04/1503/04/15144Genomicunknown
ss1695030033EVA_DECODE|EVA_DECODE_14_37343673_145152_rs12896790fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat03/02/1503/04/15144Genomicunknown
ss1711370597EVA_MGP|EVA_XIMO_486357fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat03/09/1503/09/15144Genomicunknown
ss1713437513EVA_SVP|EVA_SVP_1131880fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat03/12/1503/12/15144Genomicunknown
ss1752130354ILLUMINA|OmniExpressExome-8v1-1_B_rs12896790-131_T_R_1967886659fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat05/27/1506/09/15146Genomicunknown
ss1934411938WEILL_CORNELL_DGM|SNV:chr14:38273922fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat10/16/1510/17/15147Genomicunknown
ss1959548317ILLUMINA|14:38273922-TG-0_T_R_2299371211fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat11/13/1511/13/15147Genomicunknown
ss2027981401JJLAB|SNP8483956fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat08/29/1608/31/16149Genomicunknown
ss2094796471ILLUMINA|Immuno_BeadChip_11419691_B_rs12896790-131_T_R_1866534261fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat09/27/1609/27/16150Genomicunknown
ss2095049896ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs12896790-131_T_R_1866534261fwd/BG/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat09/27/1609/27/16150Genomicunknown
ss2156354295USC_VALOUEV|NC_000014.8:g.38273922T>Gfwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat11/17/1611/17/16150Genomicunknown
ss2201132093HUMAN_LONGEVITY|HLI-14-37804717-T-Gfwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat11/18/1611/18/16150Genomicunknown
ss2365443301TOPMED|14_38273922_T/Gfwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat11/19/1611/19/16150Genomicunknown
ss2633138865ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs12896790-131_T_R_1967886fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat02/02/1702/02/17151Genomicunknown
ss2635051136ILLUMINA|Cancer_BeadChip_11459870_A_rs12896790-128_T_R_1735634806fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat02/02/1702/02/17151Genomicunknown
ss2740677508GNOMAD|exomes_rs12896790fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat05/17/1705/17/17151Genomicunknown
ss2749125953GNOMAD|coding_rs12896790fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat05/17/1705/17/17151Genomicunknown
ss2926524574GNOMAD|rs12896790fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat05/23/1705/23/17151Genomicunknown
ss2985019789AFFY|Axiom_PsorMich_Affx-10454936fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat05/24/1705/24/17151Genomicunknown
ss3012033714SWEGEN|NC_000014.8:g.38273922T>Gfwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat05/30/1705/30/17151Genomicunknown
ss3021561388ILLUMINA|MEGA_Consortium_v2_15070954_A2_14:38273922-TG-0_T_R_2299371211fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat06/28/1706/28/17151Genomicunknown
ss3027813838BIOINF_KMB_FNS_UNIBA|14.37804717T>Gfwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat07/05/1707/05/17151Genomicunknown
ss3208496897TOPMED|TOPMed_freeze_5?chr14:37,804,717fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat10/01/1710/01/17151Genomicunknown
ss3350756439CSHL|rs12896790fwd/G/Tgtgcttaagaaggctttggatgccattctcattctgataaaggaccagat10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs12896790|allelePos=301|totalLen=601|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 AAATCCATGT CCATAAGCCT GCTTAAGTAC TGGCTTGTAG GATAGGCACC TGGGTGGGAC
 TCATGAGGGT AAGACTTCTG AACTGGGTTC TCTTCTTGTA GTGTACTGAC AAGACCTGTA
 ACTTCACCAG GTCTGTTTGT CCCCAGATAA AGTAAGAGTA GAGGTGTGTG CTCTGTGCTC
 CTTTTAACAT ATAAGGCTGT AACGTTAAAT CAATAGTGGA AAGAAACATT TCTTGCCCCC
 TCCCTGCTTT TTTATCATTA TAGGAAGCTG TGGAAGTGCT TAAGAAGGCT TTGGATGCCA
 K
 TTCTCATTCT GATAAAGGAC CAGATGCCAC AGCAATTTCA GCAGACTGTC TGTATAACTT
 GGGTCTTTGT TACATGGAGG AAGGCAATTT ACAAATGGTA TTTCGTGTAT TTAGGAGTAT
 AGATTATTTG TGATTTTAGA GACTGGTTGC TTGTATGCAA TTCTGTTTCT GAAGGCCACC
 TATACAGTGG GCAACCGGTC CAAAGCTGCT TATGAAGCTT GGCTTGTTAT AGTCATTCTG
 CACCCTGCAA CACCTAGGAC ATTGTTTTAT TTAATCAACA TGTTTTATTT GATGCTTGTT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_026437 ABBA01061537
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.
SourceG/G
G/T
T/T
HWPG
T
ss1350593077EAS 1008AF 1.00000000
EUR 1006AF 0.097399990.90260005
AFR 1322AF 0.002300000.99769998
AMR 694AF 0.049000000.95100003
SAS 978AF 0.121700000.87830001
ss137064646ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss1691457952ExAc_Aggregated_Populations121412AF 0.083929100.91607088
ss236500791pilot_1_CEU_low_coverage_panel 120AF 0.108333330.89166665
ss342385839ESP_Cohort_Populations 4550GF0.006593410.131428570.861977990.342782000.072307690.92769229
ss43583213HapMap-CEUEuropean 226IG 0.203539820.796460150.654721000.101769910.89823008
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-ASW 98IG 0.020408160.979591851.000000000.010204080.98979592
HAPMAP-GIH 176IG0.011363640.170454550.818181811.000000000.096590910.90340906
HAPMAP-MEX 100IG0.020000000.100000000.880000000.150222000.070000000.93000001
HAPMAP-MKK 286IG 0.048951050.951048971.000000000.024475520.97552449
HAPMAP-TSI 176IG0.022727270.159090910.818181810.250592000.102272730.89772725
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss491686562CSAgilent 1323GF0.006000000.180999990.812999960.342782000.096500000.90350002
ss69154466HapMap-CEUEuropean 120IG 0.216666670.783333360.751830000.108333330.89166665
HapMap-HCBAsian 90IG 1.00000000 1.00000000
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
ss96908972J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.154+/-0.2310000ALFRED: The Allele Frequency Database

  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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