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Reference SNP (refSNP) Cluster Report: rs7020673                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.3582/1794 (1000 Genomes)
C=0.3841/48225 (TOPMED)
HGVS Names
  • CM000671.2:g.4291747C>A
  • CM000671.2:g.4291747C>G
  • NC_000009.11:g.4291747C>G
  • NC_000009.12:g.4291747C>A
  • NC_000009.12:g.4291747C>G
  • NG_011782.1:g.13289G>C
  • NG_011782.1:g.13289G>T
  • NM_001042413.1:c.-98-5224G>C
  • NM_001042413.1:c.-98-5224G>T
  • XR_929206.2:n.665-5224G>C
  • XR_929206.2:n.665-5224G>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 ss280077944 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7020673 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
ss10494213BCM_SSAHASNP|chr9.NT_008413.15_4281747byFreqfwd/BC/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc06/29/0310/25/06116Genomicunknown
ss14359531WI_SSAHASNP|chr9.NT_008413.16_4281747fwd/BC/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc11/05/0311/22/03119Genomicunknown
ss15701353SC_SNP|NT_008413.16_4281747fwd/BC/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc11/17/0311/22/03120Genomicunknown
ss18004984CSHL-HAPMAP|CSHL-HuCC-200402.chr9.NT_008413.16_4281747fwd/BC/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc02/19/0403/04/04120Genomicunknown
ss22808939SSAHASNP|WGSA-200403-chr9.chr9.NT_008413.16_4281747fwd/BC/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc03/21/0403/21/04121Genomicunknown
ss24686563PERLEGEN|afd2412913byFreqfwd/BC/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc08/10/0409/13/04123Genomicunknown
ss66237885AFFY|SNP_A-4267332byFreqfwd/BC/Gctacagattgctggagaaattcaggaccttca10/27/0603/31/08127Genomicunknown
ss76383528AFFY|AFFY_6_1M_SNP_A-4267332fwd/C/Gctacagattgctggagaaattcaggaccttca08/28/0708/30/07129Genomicunknown
ss78433462HGSV|Cor12878_SNV_20070510.chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc10/17/0710/19/07129Genomicunknown
ss79051214HGSV|Cor18507_SNV_20070510.chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc10/19/0710/22/07129Genomicunknown
ss82369456KRIBB_YJKIM|KHS237476fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc11/30/0712/02/07138Genomicunknown
ss83348368HGSV|Cor18555_SNV_20070510.chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc11/27/0712/04/07130Genomicunknown
ss93999029BCMHGSC_JDW|JWB-2549006byFreqfwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc02/26/0809/05/14129Genomicunknown
ss97702077HUMANGENOME_JCVI|1103652009485fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc03/30/0803/30/08130Genomicunknown
ss1085388541000GENOMES|CEU.trio.12.15.2008_2118000_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc12/16/0812/16/08130Genomicunknown
ss1140478741000GENOMES|NA19240_2008_12_16_1916244_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc12/18/0812/18/08130Genomicunknown
ss115678082ILLUMINA-UK|NA18507_000008495_NCBI36.1_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc01/15/0901/15/09130Genomic99 %
ss139789655ENSEMBL|ENSSNP3613491fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc12/08/0810/16/09131Genomicunknown
ss143903296ENSEMBL|ENSSNP13589924fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc06/05/0906/06/09131Genomicunknown
ss163700423COMPLETE_GENOMICS|NA07022_36_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc09/29/0909/29/09132Genomicunknown
ss164348208COMPLETE_GENOMICS|NA19240_36_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc09/29/0909/29/09132Genomicunknown
ss166056823COMPLETE_GENOMICS|NA20431_36_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc09/30/0909/30/09132Genomicunknown
ss173436931AFFY|GenomeWideSNP_5_SNP_A-4267332fwd/C/Gctacagattgctggagaaattcaggaccttca10/01/0910/03/09132Genomicunknown
ss200014204BUSHMAN|BUSHMAN-chr9-4281746fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc02/16/1003/07/10132Genomicunknown
ss206773961BCM-HGSC-SUB|BCM_CMT_1011-1878933fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc03/15/1003/18/10132Genomicunknown
ss2240870781000GENOMES|pilot_1_YRI_5896761_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc04/22/1004/22/10132Genomicunknown
ss2347010151000GENOMES|pilot_1_CEU_4305644_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc05/01/1005/01/10132Genomicunknown
ss2414996731000GENOMES|pilot_1_CHB+JPT_3384750_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc05/01/1005/01/10132Genomicunknown
ss254003677BL|SNP6504_9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc08/19/1008/19/10134Genomicunknown
ss280077944GMI|GMI_AK_SNP_4398217fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc12/16/1012/16/10137Genomicunknown
ss285958436GMI|GMI_NA10851_SNP_1971209fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc12/17/1012/17/10138Genomicunknown
ss294275364PJP|SNP_3781722_chr9_4281747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc01/21/1101/21/11134Genomicunknown
ss410883194ILLUMINA|Cardio-Metabo_Chip_11395247_A_chr9_4281747rev/C/Ggagcggtgtattcctgaaggtcctgaatttctccagcaatctgtagccattatcactgtg06/07/1106/07/11135Genomicunknown
ss491419948EXOME_CHIP|.GWAS._136174_chr_9_4291747fwd/C/Gcacagtgataatggctacagattgctggagaaattcaggaccttcaggaatacaccgctc03/05/1203/05/12137Genomicunknown
ss561195357TISHKOFF|snp_chr9_4291747fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac11/22/1211/23/12138Genomicunknown
ss655624737SSMP|9_4291747fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac12/14/1202/12/15138Genomicunknown
ss986244706EVA-GONL|EVA-GONL_rs7020673fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac04/23/1404/25/14142Genomicunknown
ss1076059945JMKIDD_LAB|HGDP_WGS_chr9_4291747fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac07/10/1407/11/14142Genomicunknown
ss13326413641000GENOMES|PHASE3_V1_45100323fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac08/16/1408/16/14142Genomicunknown
ss1431730167DDI|DDI_rs7020673fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac11/04/1411/05/14144Genomicunknown
ss1582960119EVA_GENOME_DK|EVA_GENOME_DK_snv_rs7020673fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac02/19/1502/20/15144Genomicunknown
ss1595868688EVA_DECODE|EVA_DECODE_9_4281747_45306_rs7020673fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac03/02/1503/03/15144Genomicunknown
ss1622117906EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_9_4291747_24965049fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac03/04/1503/04/15144Genomicunknown
ss1665111939EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_9_4291747_24965049fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac03/04/1503/04/15144Genomicunknown
ss1713085791EVA_SVP|EVA_SVP_780158fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac03/12/1503/12/15144Genomicunknown
ss1805850303HAMMER_LAB|Hsieh_4866106fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac07/15/1507/16/15146Genomicunknown
ss1929523548WEILL_CORNELL_DGM|SNV:chr9:4291747fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac10/16/1510/17/15147Genomicunknown
ss1971139178GENOMED|rs7020673fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac02/16/1602/16/16147Genomicunknown
ss2025469056JJLAB|SNP5971611fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac08/29/1608/30/16149Genomicunknown
ss2094993246ILLUMINA|Immuno_BeadChip_11419691_B_imm_9_4281747-1_B_F_1670208668fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac09/27/1609/27/16150Genomicunknown
ss2095217573ILLUMINA|InfiniumImmunoArray-24v2-0_A_imm_9_4281747-1_B_F_2310646583fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac09/27/1609/27/16150Genomicunknown
ss2095217574ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs7020673-138_T_R_2258075275fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac09/27/1609/27/16150Genomicunknown
ss2153699352USC_VALOUEV|NC_000009.11:g.4291747C>Gfwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac11/17/1611/17/16150Genomicunknown
ss2308867170HUMAN_LONGEVITY|HLI-9-4291747-C-Gfwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac11/18/1611/18/16150Genomicunknown
ss2478860726TOPMED|9_4291747_C/Gfwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac11/20/1611/20/16150Genomicunknown
ss2627210506SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV3798921fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac01/06/1701/06/17151Genomicunknown
ss2709494624GRF|rs7020673fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac02/13/1702/13/17151Genomicunknown
ss2874706056GNOMAD|rs7020673fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac05/19/1705/19/17151Genomicunknown
ss2985454387AFFY|Axiom_PsorMich_Affx-33830015fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac05/24/1705/24/17151Genomicunknown
ss2986098174AFFY|Axiom_Smokesc1_Affx-33830015fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac05/24/1705/24/17151Genomicunknown
ss3004285972SWEGEN|NC_000009.11:g.4291747C>Gfwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac05/30/1705/30/17151Genomicunknown
ss3022902986ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs7020673-138_T_R_2258075275fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac06/28/1706/28/17151Genomicunknown
ss3026522842BIOINF_KMB_FNS_UNIBA|9.4291747C>Gfwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac07/05/1707/05/17151Genomicunknown
ss3348493579CSHL|rs7020673fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac10/02/1710/02/17151Genomicunknown
ss3580360367TOPMED|TOPMed_freeze_5?chr9:4,291,747-01fwd/A/Ctgataatggctacagattgctggagaaattcaggaccttcaggaatacac10/07/1710/07/17151Genomicunknown
ss3580360368TOPMED|TOPMed_freeze_5?chr9:4,291,747-02fwd/C/Gtgataatggctacagattgctggagaaattcaggaccttcaggaatacac10/07/1710/07/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs7020673|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/G'|mol=Genomic|build=151
 TTTATTTCTG AGTTATACCA ACTGAAGACA AATTAGTGTC CTCTGCAGGG ATTCTTCAAG
 ACCATTCTTC CAAAGACTAC TCAGAAAAGA TAATGTAATG AACATGAGGG ACCTCACCTA
 ATAGAAACTC TGACTTTGTT TTATCTGTCA ATTCGAACCT GTGCAATCTA ATCAGAGATA
 TAAATGTTTT AACTTTTCAT TTTTATATTT TATAAAATTT TCTCAAAAAT TAAAATAATC
 TTTCCTAAGT TTATAGAGTG AAAGGACTGG CCATGTCACT TTAAATTTAA ATTAATGGCT
 ATGACATTCA AAATATGGGT AGTAAATATG AACAGGACAC AGAAGAAAGA AAGGAGAGAA
 AAGGGAGAGG AAGGGAGTAG GAAAAAAAGA ATGACCACAT CCGATTCAGG AATTTACTCC
 TCTTAGTCAA TCCTCATTTA AAAATCAGAA GCAGCATTGA GAGCCTTCCA CACAGTGATA
 ATGGCTACAG ATTGCTGGAG
 V
 AAATTCAGGA CCTTCAGGAA TACACCGCTC GAGGGCAATA TTAAAAGTTC AATAACCTCT
 CTTAGAATCT CCTTTGCACT CTTCAGTGCA TCTATATAAC TTTCATATCC TCCTAGTTTA
 CTAAATGTCA CTACTTTCAC TAGTAATTAT TAGAAGTGTT TCATTTACTT TGCCCCAGTC
 ATTAACTCAT CAATGAGTAC AGAAAGGTCT AGAGAGCCAT GGTCCTACCA AAAATGGCAA
 GGGAGAAGAG GAAAATTAGG GGTTTTCTTG GTCAGTTATA AGAAATCACA CAAAATGAAA
 ACGAACTTGG AACCAAAAAG ATTTTTAAGA AAAACGTAAA TAAGTTCAGA AAGTACCATG
 CCTTGGGCCC ACAGGCTGTA AGTTCCTACA TCTACATTCA ATGAAGTATT CATTTTAAAG
 TAGTGTTTTT CAAACTGGAT TGCAATTCAT TGGTGGTCCA TGAAATTAAT TGTTCAACGG
 AGAAAGCATT ATTTAATGAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_008413 ABBA01065425
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.
SourceC/C
C/G
G/G
HWPC
G
ss115678082YRI 2IG 1.00000000 1.00000000
ss1332641364EAS 1008AF 0.495999990.50400001
EUR 1006AF 0.465200010.53479999
AFR 1322AF 0.109700000.89029998
AMR 694AF 0.417900030.58209997
SAS 978AF 0.399800000.60020000
ss139789655ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss143903296ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss163700423CEUEuropean 2IG 1.00000000 1.00000000
ss164348208YRISub-Saharan African 2IG 1.00000000 1.00000000
ss166056823PGP 2IG 1.00000000 1.00000000
ss224087078pilot_1_YRI_low_coverage_panel 118AF 0.144067790.85593218
ss234701015pilot_1_CEU_low_coverage_panel 120AF 0.458333340.54166669
ss241499673pilot_1_CHB+JPT_low_coverage_panel 120AF 0.558333340.44166666
ss24686563AFD_EUR_PANELEuropean 48IG0.250000000.333333340.416666660.150222000.416666660.58333331
AFD_AFR_PANELAfrican American 46IG0.043478260.304347810.652173941.000000000.195652170.80434781
AFD_CHN_PANELAsian 46IG0.347826090.521739130.130434780.654721000.608695630.39130434
ss66237885HapMap-CEUEuropean 118IG0.237288130.457627120.305084740.583882000.466101710.53389829
HapMap-HCBAsian 90IG0.488888890.400000010.111111110.654721000.688888910.31111112
HapMap-JPTAsian 90IG0.244444440.488888890.266666681.000000000.488888890.51111114
HapMap-YRISub-Saharan African 120IG 0.316666660.683333340.438578000.158333330.84166664
ss76383528ICMHP 4IG0.500000000.50000000 0.750000000.25000000
ss93999029HapMap-CEUEuropean 226IG0.221238940.451327440.327433620.371093000.446902660.55309737
HapMap-HCBAsian 86IG0.465116290.418604640.116279071.000000000.674418630.32558140
HapMap-JPTAsian 172IG0.232558150.453488380.313953490.438578000.459302340.54069769
HapMap-YRISub-Saharan African 226IG0.017699110.238938050.743362841.000000000.137168140.86283183
HAPMAP-ASW 98IG 0.285714300.714285730.583882000.142857150.85714287
HAPMAP-CHBAsian 82IG0.219512190.390243890.390243890.250592000.414634140.58536583
HAPMAP-CHD 170IG0.258823540.470588240.270588250.654721000.494117650.50588238
HAPMAP-GIH 174IG0.137931030.436781620.425287370.751830000.356321840.64367819
HAPMAP-LWK 180IG0.011111110.277777790.711111130.402784000.150000010.85000002
HAPMAP-MEX 100IG0.080000000.500000000.419999990.371093000.330000010.67000002
HAPMAP-MKK 282IG0.049645390.212765960.737588640.025056000.156028380.84397161
HAPMAP-TSI 176IG0.238636360.431818190.329545470.250592000.454545470.54545456
ss97702077J. Craig Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.460+/-0.1360000

  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_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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