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Reference SNP (refSNP) Cluster Report: rs4788084                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:111/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (REV)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:T=0.2997/1501 (1000 Genomes)
T=0.3495/43886 (TOPMED)
HGVS Names
  • CM000678.2:g.28528527C>T
  • NC_000016.10:g.28528527C>T
  • NC_000016.9:g.28539848C>T
  • NM_001310136.1:c.121-61625G>A
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 ss282489548 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs4788084 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
ss6607261WI_SSAHASNP|NT_010604.11_4712571byFreqfwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga02/12/0304/07/04111Genomicunknown
ss46552914PERLEGEN|PS04421186fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga08/01/0508/01/05126Genomicunknown
ss66843381ILLUMINA|HumanHap300v1.1_rs4788084fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga11/09/0611/09/06127Genomicunknown
ss67376679ILLUMINA|HumanHap550v1.1_rs4788084fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga11/14/0611/14/06127Genomicunknown
ss67756757ILLUMINA|HumanHap650Yv1.0_rs4788084fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga11/14/0611/14/06127Genomicunknown
ss70824985ILLUMINA|HumanHap550v3.0__rs4788084fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga04/20/0703/31/08130Genomicunknown
ss71406994ILLUMINA|HumanHap650Yv3.0_rs4788084fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga04/23/0704/23/07127Genomicunknown
ss75905081ILLUMINA|ILMN_Human_1M_rs4788084fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga08/28/0708/29/07129Genomicunknown
ss79195337ILLUMINA|HumanHap300v2.0_rs4788084fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga04/18/0711/18/07130Genomicunknown
ss84353109KRIBB_YJKIM|KHS691327fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga12/04/0712/07/07130Genomicunknown
ss90361401BCMHGSC_JDW|JWB-0936402byFreqrev/BC/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct02/26/0809/05/14129Genomicunknown
ss106468520BGI|BGI_rs4788084rev/BC/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct09/15/0806/18/09130Genomicunknown
ss1092936171000GENOMES|CEU.trio.12.15.2008_3281144_chr16_28447349rev/BC/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct12/16/0812/16/08130Genomicunknown
ss122388174ILLUMINA|HumanCNV370v1_C_rs4788084fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga04/14/0904/15/09131Genomicunknown
ss136653720ENSEMBL|ENSSNP6965581rev/BC/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct05/11/0905/15/09131Genomicunknown
ss154317359ILLUMINA|Human610_Quadv1_B_rs4788084-128_T_F_1501798441fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga06/18/0906/20/09131Genomicunknown
ss159494040ILLUMINA|Human660W-Quad_v1_A_rs4788084-128_T_F_1501798441fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga07/06/0907/07/09131Genomicunknown
ss168099493COMPLETE_GENOMICS|NA07022_36_chr16_28447349rev/BC/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct09/30/0909/30/09132Genomicunknown
ss171160133COMPLETE_GENOMICS|NA20431_36_chr16_28447349rev/BC/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct10/01/0910/01/09132Genomicunknown
ss171917598ILLUMINA|HumanCNV370-Quadv3_C_rs4788084-128_T_F_1501798441fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga10/01/0910/04/09132Genomicunknown
ss173813414ILLUMINA|Human1M-Duov3_B_rs4788084-128_T_F_1501798441fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga10/01/0910/04/09132Genomicunknown
ss201600521BUSHMAN|BUSHMAN-chr16-28447348rev/BC/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct02/16/1003/08/10132Genomicunknown
ss2272112941000GENOMES|pilot_1_YRI_9020977_chr16_28447349rev/C/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct04/22/1004/22/10132Genomicunknown
ss2370023121000GENOMES|pilot_1_CEU_6606941_chr16_28447349rev/C/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct05/01/1005/01/10132Genomicunknown
ss2433467801000GENOMES|pilot_1_CHB+JPT_5231857_chr16_28447349rev/C/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct05/01/1005/01/10132Genomicunknown
ss255613137BL|SNP38574_16_28447349rev/BC/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct08/20/1008/20/10134Genomicunknown
ss282489548GMI|GMI_AK_SNP_6809949rev/C/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct12/16/1012/16/10137Genomicunknown
ss287057389GMI|GMI_NA10851_SNP_3070180rev/C/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct12/17/1012/17/10138Genomicunknown
ss291943271PJP|SNP_1449629_chr16_28447349rev/C/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct01/21/1101/21/11134Genomicunknown
ss410815782ILLUMINA|Cardio-Metabo_Chip_11395247_A_chr16_28447349fwd/TA/Gagggagttctgtggccttcagggagtcccagggagcaagattagagcacccagtccctga06/07/1106/07/11135Genomicunknown
ss491506649EXOME_CHIP|.GWAS._222875_chr_16_28539848rev/BC/Ttcagggactgggtgctctaatcttgctccctgggactccctgaaggccacagaactccct03/05/1203/05/12137Genomicunknown
ss537274322ILLUMINA|HumanOmni5-4v1_B_rs4788084-131_T_F_1908441576rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac06/22/1208/29/15146Genomicunknown
ss564864446TISHKOFF|snp_chr16_28539848rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac11/22/1211/23/12138Genomicunknown
ss660616536SSMP|16_28539848rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac12/14/1202/14/15138Genomicunknown
ss780685352ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs4788084-131_T_F_1990492598rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac05/30/1307/10/15146Genomicunknown
ss783358838ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs4788084-131_T_F_1990492598rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac05/31/1306/19/15146Genomicunknown
ss825525855ILLUMINA|HumanCNV370v1_C_rs4788084-126_T_F_IFB1137737102:0rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac06/24/1311/21/14144Genomicunknown
ss992420067EVA-GONL|EVA-GONL_rs4788084rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac04/23/1404/30/14142Genomicunknown
ss1080583237JMKIDD_LAB|HGDP_WGS_chr16_28539848rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac07/10/1407/12/14142Genomicunknown
ss13559202661000GENOMES|PHASE3_V1_69347887rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac08/16/1408/16/14142Genomicunknown
ss1427820389DDI|DDI_rs4788084rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac11/04/1411/04/14144Genomicunknown
ss1577891180EVA_GENOME_DK|EVA_GENOME_DK_snv_rs4788084rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac02/19/1502/19/15144Genomicunknown
ss1634283117EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_16_28539848_38345684rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac03/04/1503/04/15144Genomicunknown
ss1677277150EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_16_28539848_38345684rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac03/04/1503/04/15144Genomicunknown
ss1696454742EVA_DECODE|EVA_DECODE_16_28447349_249030_rs4788084rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac03/02/1503/04/15144Genomicunknown
ss1713535371EVA_SVP|EVA_SVP_1229738rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac03/12/1503/12/15144Genomicunknown
ss1917906338ILLUMINA|HumanExome-12v1-1_B_exm-rs4788084-131_T_F_1990492598rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac10/16/1510/16/15147Genomicunknown
ss1935843934WEILL_CORNELL_DGM|SNV:chr16:28539848rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac10/16/1510/19/15147Genomicunknown
ss1959671672ILLUMINA|exm-rs4788084-131_T_F_1990492598rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac11/13/1511/13/15147Genomicunknown
ss1968249397GENOMED|rs4788084rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac02/16/1602/16/16147Genomicunknown
ss2028710284JJLAB|SNP9212839rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac08/29/1608/31/16149Genomicunknown
ss2094889063ILLUMINA|Immuno_BeadChip_11419691_B_imm_16_28447349-1_T_R_1670088391rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac09/27/1609/27/16150Genomicunknown
ss2095065259ILLUMINA|InfiniumImmunoArray-24v2-0_A_imm_16_28447349-1_T_R_2310672134rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac09/27/1609/27/16150Genomicunknown
ss2095065260ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs4788084-138_T_F_2264361531rev/BC/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac09/27/1609/27/16150Genomicunknown
ss2157122887USC_VALOUEV|NC_000016.9:g.28539848C>Trev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac11/17/1611/17/16150Genomicunknown
ss2211647930HUMAN_LONGEVITY|HLI-16-28528527-C-Trev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac11/18/1611/18/16150Genomicunknown
ss2376403216TOPMED|16_28539848_C/Trev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac11/19/1611/19/16150Genomicunknown
ss2628847871SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV5874978rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac01/06/1701/06/17151Genomicunknown
ss2633310628ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs4788084-131_T_F_19084415rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac02/02/1702/02/17151Genomicunknown
ss2633310629ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs4788084-131_T_F_2130rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac02/02/1702/02/17151Genomicunknown
ss2701628979GRF|rs4788084rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac02/13/1702/13/17151Genomicunknown
ss2941913654GNOMAD|rs4788084rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac05/23/1705/23/17151Genomicunknown
ss2985065077AFFY|Axiom_PsorMich_Affx-12618862rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac05/24/1705/24/17151Genomicunknown
ss2985702847AFFY|Axiom_Smokesc1_Affx-12618862rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac05/24/1705/24/17151Genomicunknown
ss3014306017SWEGEN|NC_000016.9:g.28539848C>Trev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac05/30/1705/30/17151Genomicunknown
ss3021697889ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs4788084-131_T_F_1990492598rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac06/28/1706/28/17151Genomicunknown
ss3028178855BIOINF_KMB_FNS_UNIBA|16.28528527C>Trev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac07/05/1707/05/17151Genomicunknown
ss3243751823TOPMED|TOPMed_freeze_5?chr16:28,528,527rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac10/01/1710/01/17151Genomicunknown
ss3351402757CSHL|rs4788084rev/C/Tgactgggtgctctaatcttgctccctgggactccctgaaggccacagaac10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs4788084|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 ACCTTGGTTT GTATATAAAA ATATTATCCA GGATGGTGGC TCACGCCTGT AATCCCAGCA
 CTTCGGGAGG CCAAGGCGGG CAGATCACCT GAGGTCAGGA GTTCAAGACC AGCTTCGTCA
 ACATAGCGAA ACCCCGTCTC TACTAAAAAT ACAAAAATTA GCCAGGCTTG GTGGCTCGTG
 CCTATAATCA CAGCTACTAG GGAGGCTGAT GCACAAGAAT TGCTTGAACC CAGGAGGCAA
 AGGTTGCACT GAGCCGAGAA CACTCCACTG CACTCCACTG AGCCACTGCA CTCCAGCCTG
 GGAGTGAGAC TGCCTAAAAA AAAAAAAAAT CTAGCCACAG CCATTATTAT CACACTGGAT
 ATTTACCAAA GCCTGCACTA GGGAAAAACA CCTGGGTCAC GGGTTCACTG CTGGTTGGAG
 GCTGAGCCAA GAGCAAACTA AGTGTGCTGA TACCCATGCC CCTGATTTCT AGGGAGTTCT
 GTGGCCTTCA GGGAGTCCCA
 R
 GGGAGCAAGA TTAGAGCACC CAGTCCCTGA GTGCCCTGCT ATCAGCGGCC TTGACAGAGG
 CGATCTCTCC TTGGTGGCTG GAATCAGCAT CCAGGGCTCT GTCAACTATT AGAGAAACAT
 TTTATTCTTT TTGTAAAACA AAAGTTCTCT TTTCTTTTCT GATTACAAAA GAAGTTATTG
 CTGTGGAATC GCAAGATAAT CCCCATCCTC TGGTCTGTCT GTCCTTTGTT CCCATGACTG
 AACTCCAACT TTTGCAAAAC ACTTACTTTT ATTTTATGTT TTATTCTAGA GACAGGCTCT
 TGCTCTGCTG CCCAGGCTGG AGTGCAGTGG TGTAATCTCG GCTCACTGAA GCTTTGACCT
 CCAGGGTCTC AAGTGATCCT CCCACCTCAG CCTCCTGAGT AGCTGGGACT ACAGGCACAC
 GTCACCACAC CCTAATTTTT GTATATACAC ACACACACAC ACATATATAC GTATATATAT
 GTGTGCGTAT ATGTGTGTGT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000016.5
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs4788084 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceA/A
A/G
G/G
HWPA
G
ss1355920266EAS 1008AF 0.285699990.71429998
EUR 1006AF 0.353900020.64610004
AFR 1322AF 0.226900000.77310002
AMR 694AF 0.489899990.51010001
SAS 978AF 0.221900000.77810001
ss136653720ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss168099493CEUEuropean 2IG 1.00000000 0.500000000.50000000
ss171160133PGP 2IG1.00000000 1.00000000
ss201600521BANTU 2IG 1.00000000 0.500000000.50000000
ss227211294pilot_1_YRI_low_coverage_panel 118AF 0.186440680.81355929
ss237002312pilot_1_CEU_low_coverage_panel 120AF 0.366666670.63333333
ss243346780pilot_1_CHB+JPT_low_coverage_panel 120AF 0.241666660.75833333
ss90361401HapMap-CEUEuropean 222IG0.126126130.513513510.360360350.371093000.382882890.61711711
HapMap-HCBAsian 84IG0.071428570.285714300.642857130.342782000.214285720.78571427
HapMap-JPTAsian 170IG0.035294120.376470600.588235320.438578000.223529410.77647060
HapMap-YRISub-Saharan African 226IG0.017699110.336283180.646017670.250592000.185840710.81415927
HAPMAP-ASW 98IG0.040816330.448979590.510204080.294266000.265306120.73469388
HAPMAP-CHBAsian 82IG0.048780490.341463420.609756111.000000000.219512190.78048778
HAPMAP-CHD 170IG0.082352940.411764710.505882381.000000000.288235310.71176469
HAPMAP-GIH 176IG0.147727270.363636370.488636370.099721000.329545470.67045456
HAPMAP-LWK 180IG0.055555560.344444450.600000021.000000000.227777780.77222222
HAPMAP-MEX 100IG0.180000010.519999980.300000010.751830000.440000000.56000000
HAPMAP-MKK 284IG0.091549290.401408460.507042230.751830000.292253520.70774651
HAPMAP-TSI 176IG0.136363640.363636370.500000000.150222000.318181810.68181819
ENSEMBL_Venter 2IG 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.420+/-0.1840000ALFRED: 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
byClusterbyFreqwith2hitWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNPNCBI
UNKNOWNUNKNOWNUNKNOWN

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