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Reference SNP (refSNP) Cluster Report: rs2074480                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:96/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C (REV)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.1909/956 (1000 Genomes)
G=0.1790/22481 (TOPMED)
HGVS Names
  • CM000668.2:g.30073033T>G
  • NC_000006.11:g.30040810T>G
  • NC_000006.12:g.30073033T>G
  • NM_025236.3:c.682+124A>C
  • NM_170769.2:c.682+124A>C
  • NT_113891.3:g.1552804T>G
  • NT_167244.1:g.1281041T>G
  • NT_167244.2:g.1331125T>G
  • NT_167245.1:g.1334534T>G
  • NT_167245.2:g.1328949T>G
  • NT_167246.1:g.1339403T>G
  • NT_167246.2:g.1333783T>G
  • NT_167247.1:g.1422708T>G
  • NT_167247.2:g.1417123T>G
  • NT_167248.1:g.1333784G=
  • NT_167248.1:g.1333784G>T
  • NT_167248.2:g.1328188G=
  • NT_167248.2:g.1328188G>T
  • NT_167249.1:g.1371250T>G
  • NT_167249.2:g.1371952T>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 ss278713859 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2074480 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
ss2989143YUSUKE|IMS-JST001345byFreqfwd/TA/Catgtctgcattagtttcctagtactgctctatgaagcaccgcaaagtaggtggctgaaac05/24/0110/25/0696Genomicunknown
ss12682678SI_MHC_SNP|AL669914.2_67666_TGbyFreqrev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat09/10/0310/21/04118Genomicunknown
ss23306328PERLEGEN|afd4532767byFreqrev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat08/10/0409/13/04123Genomicunknown
ss66579731ILLUMINA|HumanHap300v1.1_rs2074480fwd/BA/Catgtctgcattagtttcctagtactgctctatgaagcaccgcaaagtaggtggctgaaac11/09/0611/09/06127Genomicunknown
ss67222671ILLUMINA|HumanHap550v1.1_rs2074480fwd/TA/Catgtctgcattagtttcctagtactgctctatgaagcaccgcaaagtaggtggctgaaac11/14/0611/14/06127Genomicunknown
ss67617139ILLUMINA|HumanHap650Yv1.0_rs2074480fwd/TA/Catgtctgcattagtttcctagtactgctctatgaagcaccgcaaagtaggtggctgaaac11/14/0611/14/06127Genomicunknown
ss70700962ILLUMINA|HumanHap550v3.0__rs2074480rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat04/20/0703/30/08130Genomicunknown
ss71267033ILLUMINA|HumanHap650Yv3.0_rs2074480fwd/TA/Catgtctgcattagtttcctagtactgctctatgaagcaccgcaaagtaggtggctgaaac04/23/0704/23/07127Genomicunknown
ss74929240ILLUMINA|ILMN_Human_1M_rs2074480fwd/TA/Catgtctgcattagtttcctagtactgctctatgaagcaccgcaaagtaggtggctgaaac08/28/0708/29/07129Genomicunknown
ss79112784ILLUMINA|HumanHap300v2.0_rs2074480fwd/TA/Catgtctgcattagtttcctagtactgctctatgaagcaccgcaaagtaggtggctgaaac04/18/0711/18/07130Genomicunknown
ss83966393KRIBB_YJKIM|KHS586747fwd/TA/Catgtctgcattagtttcctagtactgctctatgaagcaccgcaaagtaggtggctgaaac12/04/0712/06/07130Genomicunknown
ss104293439BGI|BGI_rs2074480rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat06/08/0806/18/09131Genomicunknown
ss1141103841000GENOMES|NA19240_2008_12_16_1330987_chr6_30148789rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat12/18/0812/18/08137Genomicunknown
ss116381997ILLUMINA-UK|NA18507_000045268_NCBI36.1_chr6_30148789rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat01/17/0901/17/09130Genomic99 %
ss121910335ILLUMINA|HumanCNV370v1_C_rs2074480fwd/TA/Catgtctgcattagtttcctagtactgctctatgaagcaccgcaaagtaggtggctgaaac04/14/0904/14/09131Genomicunknown
ss153846313ILLUMINA|Human610_Quadv1_B_rs2074480-128_B_R_1501707248rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat06/18/0906/20/09131Genomicunknown
ss159356573ILLUMINA|Human660W-Quad_v1_A_rs2074480-128_B_R_1501707248rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat07/06/0907/07/09131Genomicunknown
ss160498902ILLUMINA|HumanOmni1-Quad_v1-0_B_rs2074480-128_B_R_1501707248rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat08/04/0910/02/09131Genomicunknown
ss163317509COMPLETE_GENOMICS|NA19240_36_chr6_30148789rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat09/29/0909/29/09132Genomicunknown
ss171002390ILLUMINA|HumanCNV370-Quadv3_C_rs2074480-128_B_R_1501707248rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat10/01/0910/03/09132Genomicunknown
ss173100695ILLUMINA|Human1M-Duov3_B_rs2074480-128_B_R_1501707248rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat10/01/0910/03/09132Genomicunknown
ss201596170BUSHMAN|BUSHMAN-chr6-30148788byFreqrev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat02/16/1009/05/14132Genomicunknown
ss2222913561000GENOMES|pilot_1_YRI_4101039_chr6_30148789rev/G/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat04/22/1004/22/10137Genomicunknown
ss2333866231000GENOMES|pilot_1_CEU_2991252_chr6_30148789rev/G/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat05/01/1005/01/10137Genomicunknown
ss2404584501000GENOMES|pilot_1_CHB+JPT_2343527_chr6_30148789rev/G/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat05/01/1005/01/10137Genomicunknown
ss278713859GMI|GMI_AK_SNP_3034098rev/G/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat12/16/1012/16/10137Genomicunknown
ss410919102ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs2074480rev/BG/Tgtttcagccacctactttgcggtgcttcatagagcagtactaggaaactaatgcagacat06/07/1106/07/11137Genomicunknown
ss480413568ILLUMINA|HumanOmni2.5-4v1_B_rs2074480-128_B_R_1773296097rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca01/30/1210/28/16137Genomicunknown
ss480426989ILLUMINA|HumanOmniExpress-12v1_C_rs2074480-131_B_R_1857107362rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca01/30/1210/27/16137Genomicunknown
ss481210270ILLUMINA|HumanOmni1-Quad_v1-0_C_rs2074480-131_B_R_1865461330rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca01/30/1208/28/15146Genomicunknown
ss485004299ILLUMINA|HumanOmni2.5-4v1_D_rs2074480-131_B_R_1857107362rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca01/30/1210/28/16137Genomicunknown
ss537035148ILLUMINA|HumanOmni5-4v1_B_rs2074480-131_B_R_1911651537rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca06/22/1208/29/15146Genomicunknown
ss559101208TISHKOFF|snp_chr6_30040810rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca11/22/1211/23/12138Genomicunknown
ss653018003SSMP|6_30040810rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca12/14/1202/11/15138Genomicunknown
ss778853505ILLUMINA|HumanOmni25Exome-8v1_A_rs2074480-131_B_R_1865461330rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca05/30/1307/09/15142Genomicunknown
ss782948466ILLUMINA|HumanOmni2.5-4v1_H_rs2074480-131_B_R_1857107362rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca05/30/1307/28/15146Genomicunknown
ss783910826ILLUMINA|HumanOmniExpressExome-8v1_A_rs2074480-131_B_R_1911651537rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca05/31/1306/19/15142Genomicunknown
ss825443302ILLUMINA|HumanCNV370v1_C_rs2074480-123_B_R_IFB1151451336:0rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca06/24/1311/21/14144Genomicunknown
ss832204352ILLUMINA|HumanOmniExpress-12v1_H_rs2074480-131_B_R_1857107362rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca09/17/1306/19/15146Genomicunknown
ss834314190ILLUMINA|HumanOmni2.5-8v1_A_rs2074480-131_B_R_1865461330rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca09/18/1307/28/15142Genomicunknown
ss982743251EVA-GONL|EVA-GONL_rs2074480rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca04/23/1404/24/14142Genomicunknown
ss1073491964JMKIDD_LAB|HGDP_WGS_chr6_30040810rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca07/10/1407/11/14142Genomicunknown
ss13195096101000GENOMES|PHASE3_V1_31439322rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca08/16/1408/16/14142Genomicunknown
ss1397447430HAMMER_LAB|HAMMER_LAB_rs2074480rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca09/30/1409/30/14146Genomicunknown
ss1581595611EVA_GENOME_DK|EVA_GENOME_DK_snv_rs2074480rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca02/19/1502/20/15144Genomicunknown
ss1592290670EVA_DECODE|EVA_DECODE_6_30148789_254708_rs2074480rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca03/02/1503/03/15144Genomicunknown
ss1615249239EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_6_30040810_17435493rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca03/04/1503/04/15144Genomicunknown
ss1658243272EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_6_30040810_17435493rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca03/04/1503/04/15144Genomicunknown
ss1711118722EVA_MGP|EVA_XIMO_234482rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca03/09/1503/09/15144Genomicunknown
ss1712848454EVA_SVP|EVA_SVP_542821rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca03/12/1503/12/15144Genomicunknown
ss1752625088ILLUMINA|OmniExpressExome-8v1-1_B_rs2074480-131_B_R_1911651537rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca05/27/1506/09/15146Genomicunknown
ss1804347284HAMMER_LAB|Hsieh_3357116rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca07/15/1507/15/15146Genomicunknown
ss1925995372WEILL_CORNELL_DGM|SNV:chr6:30040810rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca10/16/1510/17/15147Genomicunknown
ss1958880780ILLUMINA|1kg_6_30148789-1_T_R_2304703966rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca11/13/1511/13/15147Genomicunknown
ss1970350013GENOMED|rs2074480rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca02/16/1602/16/16147Genomicunknown
ss2023625919JJLAB|SNP4128474rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca08/29/1608/30/16149Genomicunknown
ss2094951511ILLUMINA|Immuno_BeadChip_11419691_B_1kg_6_30148789-1_T_R_1767784859rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca09/27/1609/27/16150Genomicunknown
ss2095174100ILLUMINA|InfiniumImmunoArray-24v2-0_A_1kg_6_30148789-1_T_R_2310733617rev/BG/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca09/27/1609/27/16150Genomicunknown
ss2151791208USC_VALOUEV|NC_000006.11:g.30040810T>Grev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca11/17/1611/17/16151Genomicunknown
ss2282867790HUMAN_LONGEVITY|HLI-6-30073033-T-Grev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca11/18/1611/18/16150Genomicunknown
ss2451237621TOPMED|6_30040810_T/Grev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca11/20/1611/20/16150Genomicunknown
ss2626299068SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV2631842rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca01/06/1701/06/17151Genomicunknown
ss2634424024ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs2074480-131_B_R_19116515rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca02/02/1702/02/17151Genomicunknown
ss2707383328GRF|rs2074480rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca02/13/1702/13/17151Genomicunknown
ss2837306244GNOMAD|rs2074480rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca05/18/1705/18/17151Genomicunknown
ss2985990475AFFY|Axiom_Smokesc1_Affx-28422862rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca05/24/1705/24/17151Genomicunknown
ss2998763892SWEGEN|NC_000006.11:g.30040810T>Grev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca05/30/1705/30/17151Genomicunknown
ss3022592544ILLUMINA|MEGA_Consortium_v2_15070954_A2_1kg_6_30148789-1_T_R_2304703966rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca06/28/1706/28/17151Genomicunknown
ss3025598089BIOINF_KMB_FNS_UNIBA|6.30073033T>Grev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca07/05/1707/05/17151Genomicunknown
ss3493584526TOPMED|TOPMed_freeze_5?chr6:30,073,033rev/G/Tagccacctactttgcggtgcttcatagagcagtactaggaaactaatgca10/05/1710/05/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2074480|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=151
 GCCCCAGGGA ATGAAGCCCA GAGCTCACAT CCATGTTTGT TTCTGCCCAT CCTAGGATAT
 GAGGAAGACA TGGAGACGGT GAGTTCCACT TTTCTGTTCC CTCCTTTTCT CACCAGCTGC
 CATAGCCATC ACGTTCTCAC TGGGCCCACA CCTTTGTTCC CATTAATAGG CAGGTTTTCT
 GGGGTATAGT CTCATCCCTT CTTCCTCCAG AGATGTGAGT GGGGTATGCG TGGGGGCATT
 AGGATCAGAG GGCTGATTTC CTGACCCTTC CCCTCATCTG TGTAGATTTG AAGTCCCAAC
 ATCCAAGTCA TCTAATTCAG AGGATGATCT CCCTGAAGAT TATCCAGTGG TCAAAAAAAT
 GCTTCATAGA CTGACAGGTA AGGAAAGAAG AAGGGAGGGA AGGGAATTGA ATGAAAGTCT
 GTGTTAGATT TTCTTCCTTT TAGCCCTAAA AAGTGATCAG GTCCTTTTTG ATGTCTGCAT
 TAGTTTCCTA GTACTGCTCT
 M
 ATGAAGCACC GCAAAGTAGG TGGCTGAAAC AACAGACATT TATCTCAAAG TTCAGGAGGT
 AGAAGTCTGA AATCAAGGTG TCAGCAGTGT TGGTTCCTTC TGACGGCCAT GAGACAGAAT
 CTGTTCCATG CCTGTCTCCT AGCCTCTGGT AGCCTCACAT GTTCTTTGGG TGATAGGTCT
 GCACATTTTC TTTTGTATGC ATTTGTCTCT GTGTCCAAAT TTCCTCTTTT TGTAAGTCAG
 CAATCTGGAT TAGAGCCCAC CCTAATGACC TTCATTTTAA CTTGATTACC TATGTAAAGA
 TCCTGTTTCA AAACAAGGTA ACATTCTGAG GTTTGGAGGA CTTCAACCTA TCTTTGTGTG
 TGTGTGTGGA GTGGGGGAGG GCACAGTTCA GCCTATAACA ATGTCTATCC TCGATTCCTC
 ATATTCCAGC CATTTTCCCT CTTCCTTTTT CATACATTCA AACAACAGAT CCCTGAAGGT
 TAGGTGCCTC TCAAAAATCT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000006.6
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs2074480 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/C
C/C
HWPA
C
ss116381997YRI 2IG 1.00000000 0.500000000.50000000
ss12682678HapMap-CEUEuropean 226IG0.858407080.132743360.008849560.654721000.924778760.07522124
HapMap-HCBAsian 86IG0.581395330.395348850.023255810.342782000.779069780.22093023
HapMap-JPTAsian 172IG0.453488380.465116290.081395350.479500000.686046540.31395349
HapMap-YRISub-Saharan African 224IG0.428571430.500000000.071428570.150222000.678571400.32142857
HAPMAP-ASW 98IG0.428571430.530612230.040816330.099721000.693877580.30612245
HAPMAP-CHBAsian 80IG0.699999990.275000010.025000001.000000000.837499980.16249999
HAPMAP-CHD 170IG0.788235310.176470590.035294120.099721000.876470570.12352941
HAPMAP-GIH 176IG0.784090940.193181810.022727270.479500000.880681810.11931818
HAPMAP-LWK 178IG0.505617980.426966280.067415730.654721000.719101130.28089887
HAPMAP-MEX 100IG0.500000000.400000010.100000000.751830000.699999990.30000001
HAPMAP-MKK 286IG0.503496530.426573430.069930070.583882000.716783230.28321677
HAPMAP-TSI 176IG0.670454560.318181810.011363640.250592000.829545440.17045455
ss1319509610EAS 1008AF 0.811500010.18850000
EUR 1006AF 0.904599960.09540000
AFR 1322AF 0.701200010.29880002
AMR 694AF 0.825599970.17440000
SAS 978AF 0.842500030.15750000
ss163317509YRISub-Saharan African 2IG 1.00000000 1.00000000
ss201596170BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
BANTU 2IG 1.00000000 0.500000000.50000000
ss222291356pilot_1_YRI_low_coverage_panel 118AF 0.694915240.30508474
ss23306328AFD_EUR_PANELEuropean 38IG0.842105270.15789473 1.000000000.921052630.07894737
AFD_AFR_PANELAfrican American 32IG0.687500000.187500000.125000000.099721000.781250000.21875000
AFD_CHN_PANELAsian 44IG0.863636370.13636364 1.000000000.931818190.06818182
ss233386623pilot_1_CEU_low_coverage_panel 120AF 0.908333360.09166667
ss240458450pilot_1_CHB+JPT_low_coverage_panel 120AF 0.708333310.29166666
ss2989143JBIC-allele 1086AF 0.709100010.29089999

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.309+/-0.2430000ALFRED: 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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