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Reference SNP (refSNP) Cluster Report: rs3099950                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:103/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS PheGenI
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/G (FWD)
Allele Origin:
Ancestral Allele:G
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.1211/2779 (ExAC)
A=0.0697/349 (1000 Genomes)
A=0.0896/409 (GO-ESP)
A=0.0791/9937 (TOPMED)
HGVS Names
  • CM000664.2:g.38882417G>A
  • NC_000002.11:g.39109558G>A
  • NC_000002.12:g.38882417G>A
  • NM_001145450.1:c.142G>A
  • NP_001138922.1:p.Glu48Lys
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 ss166456430 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3099950 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
ss4337587SC_JCM|AC018693.8_117920byFreqfwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag02/19/0203/31/08103Genomicunknown
ss66648008ILLUMINA|HumanHap300v1.1_rs3099950fwd/BA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag11/09/0611/09/06127Genomicunknown
ss67289905ILLUMINA|HumanHap550v1.1_rs3099950fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag11/14/0611/14/06127Genomicunknown
ss67693316ILLUMINA|HumanHap650Yv1.0_rs3099950fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag11/14/0611/14/06127Genomicunknown
ss70768479ILLUMINA|HumanHap550v3.0__rs3099950rev/BC/Tcttggatatcagtatattccccttcaccttcaccctgcaatagtagaaaataagttttcc04/20/0703/30/08130Genomicunknown
ss71343434ILLUMINA|HumanHap650Yv3.0_rs3099950fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag04/23/0704/23/07127Genomicunknown
ss74820347AFFY|SNP_M-322870fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag08/09/0708/09/07128Genomicunknown
ss75493289ILLUMINA|ILMN_Human_1M_rs3099950fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag08/28/0708/29/07129Genomicunknown
ss79158105ILLUMINA|HumanHap300v2.0_rs3099950fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag04/18/0711/18/07130Genomicunknown
ss84147078KRIBB_YJKIM|KHS645310fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag12/04/0712/06/07130Genomicunknown
ss1094263391000GENOMES|CEU.trio.12.15.2008_357206_chr2_38963062fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag12/16/0812/16/08130Genomicunknown
ss122168779ILLUMINA|HumanCNV370v1_C_rs3099950fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag04/14/0904/15/09131Genomicunknown
ss154253526ILLUMINA|Human610_Quadv1_B_rs3099950-128_B_R_1501752612rev/BC/Tcttggatatcagtatattccccttcaccttcaccctgcaatagtagaaaataagttttcc06/18/0906/20/09131Genomicunknown
ss159430335ILLUMINA|Human660W-Quad_v1_A_rs3099950-128_B_R_1501752612rev/BC/Tcttggatatcagtatattccccttcaccttcaccctgcaatagtagaaaataagttttcc07/06/0907/07/09131Genomicunknown
ss161074833ILLUMINA|HumanOmni1-Quad_v1-0_B_SNP2-38963062-0_B_R_1588073677rev/BC/Tcttggatatcagtatattccccttcaccttcaccctgcaatagtagaaaataagttttcc08/04/0910/05/09131Genomicunknown
ss166456430COMPLETE_GENOMICS|NA20431_36_chr2_38963062fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag09/30/0909/30/09132Genomicunknown
ss171536042ILLUMINA|HumanCNV370-Quadv3_C_rs3099950-128_B_R_1501752612rev/BC/Tcttggatatcagtatattccccttcaccttcaccctgcaatagtagaaaataagttttcc10/01/0910/04/09132Genomicunknown
ss173560941ILLUMINA|Human1M-Duov3_B_rs3099950-128_B_R_1501752612rev/BC/Tcttggatatcagtatattccccttcaccttcaccctgcaatagtagaaaataagttttcc10/01/0910/04/09132Genomicunknown
ss2311249221000GENOMES|pilot_1_CEU_729551_chr2_38963062fwd/A/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag05/01/1005/01/10132Genomicunknown
ss253049349BL|SNP46517_2_38963062fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag08/18/1008/18/10134Genomicunknown
ss479172396ILLUMINA|HumanOmni1-Quad_v1-0_C_kgp1116721-0_B_R_1811869929fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat01/30/1208/28/15146Genomicunknown
ss491317960EXOME_CHIP|nonsyn_34187_chr_2_39109558fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag03/05/1203/05/12137Genomicunknown
ss491782137CLINSEQ_SNP|SNV-chr2-38963062byFreqfwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat03/06/1209/05/14137Genomicunknown
ss537161244ILLUMINA|HumanOmni5-4v1_B_rs3099950-131_B_R_1885470154fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat06/22/1208/28/15146Genomicunknown
ss649077288SSMP|2_39109558fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat12/14/1202/10/15138Genomicunknown
ss712409887NHLBI-ESP|ESP6500SI-chr2-39109558fwd/TA/Gggaaaacttattttctactattgcagggtgaaggtgaaggggaatatactgatatccaag02/20/1302/20/13138Genomicunknown
ss780776179ILLUMINA|HumanOmni25Exome-8v1_A_exm188225-0_B_R_1918918228fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat05/30/1307/09/15146Genomicunknown
ss783456136ILLUMINA|HumanOmniExpressExome-8v1_A_exm188225-0_B_R_1918918228fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat05/31/1306/19/15146Genomicunknown
ss825488623ILLUMINA|HumanCNV370v1_C_rs3099950-103_B_R_IFB1135580881:0fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat06/24/1311/21/14147Genomicunknown
ss976711671EVA-GONL|EVA-GONL_rs3099950fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat04/23/1404/23/14142Genomicunknown
ss1069025306JMKIDD_LAB|HGDP_WGS_chr2_39109558fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat07/10/1407/10/14142Genomicunknown
ss12967626301000GENOMES|PHASE3_V1_7732287fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat08/16/1408/16/14142Genomicunknown
ss1397288736HAMMER_LAB|HAMMER_LAB_rs3099950fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat09/30/1409/30/14146Genomicunknown
ss1578831361EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3099950fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat02/19/1502/20/15144Genomicunknown
ss1586119228EVA_DECODE|EVA_DECODE_2_38963062_321118_rs3099950fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat03/02/1503/02/15144Genomicunknown
ss1603262717EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_39109558_4272742fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat03/04/1503/04/15144Genomicunknown
ss1646256750EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_39109558_4272742fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat03/04/1503/04/15144Genomicunknown
ss1686275507EVA_EXAC|EVA_EXAC_1139251fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat03/04/1503/04/15144Genomicunknown
ss1710960560EVA_MGP|EVA_XIMO_77312fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat03/09/1503/09/15144Genomicunknown
ss1712447311EVA_SVP|EVA_SVP_141863fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat03/12/1503/12/15144Genomicunknown
ss1752355739ILLUMINA|OmniExpressExome-8v1-1_B_exm188225-0_B_R_2058870892fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat05/27/1506/09/15146Genomicunknown
ss1917748376ILLUMINA|HumanExome-12v1-1_B_exm188225-0_B_R_2058870892fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat10/16/1510/16/15147Genomicunknown
ss1919946242WEILL_CORNELL_DGM|SNV:chr2:39109558fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat10/16/1510/16/15147Genomicunknown
ss1946038026ILLUMINA|HumanCoreExome-12v1-0_C_exm188225-0_B_R_2058870892fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat10/29/1510/29/15147Genomicunknown
ss1958409042ILLUMINA|exm188225-0_B_R_1918918228fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat11/13/1511/13/15147Genomicunknown
ss1968744512GENOMED|rs3099950fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat02/16/1602/16/16147Genomicunknown
ss2020505560JJLAB|SNP1008115fwd/TA/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat08/29/1608/30/16149Genomicunknown
ss2148549967USC_VALOUEV|NC_000002.11:g.39109558G>Afwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat11/17/1611/17/16150Genomicunknown
ss2229280020HUMAN_LONGEVITY|HLI-2-38882417-G-Afwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat11/18/1611/18/16150Genomicunknown
ss2395205403TOPMED|2_39109558_G/Afwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat11/19/1611/19/16150Genomicunknown
ss2633599711ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs3099950-131_B_R_18854701fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat02/02/1702/02/17151Genomicunknown
ss2633599712ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs3099950-131_B_R_2130fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat02/02/1702/02/17151Genomicunknown
ss2732614898GNOMAD|exomes_rs3099950fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat05/17/1705/17/17151Genomicunknown
ss2746665177GNOMAD|coding_rs3099950fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat05/17/1705/17/17151Genomicunknown
ss2772128518GNOMAD|rs3099950fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat05/17/1705/17/17151Genomicunknown
ss2985165263AFFY|Axiom_PsorMich_Affx-20019935fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat05/24/1705/24/17151Genomicunknown
ss2989322405SWEGEN|NC_000002.11:g.39109558G>Afwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat05/30/1705/30/17151Genomicunknown
ss3021961550ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm188225-0_B_R_1918918228fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat06/28/1706/28/17151Genomicunknown
ss3024018153BIOINF_KMB_FNS_UNIBA|2.38882417G>Afwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat07/05/1707/05/17151Genomicunknown
ss3304804243TOPMED|TOPMed_freeze_5?chr2:38,882,417fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat10/02/1710/02/17151Genomicunknown
ss3344177028CSHL|rs3099950fwd/A/Gacttattttctactattgcagggtgaaggtgaaggggaatatactgatat10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3099950|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/G'|mol=Genomic|build=151
 CCTAAAATCT TGGACACCAA ATAATTGTTT GTTTTTGTTT GGAATAGTAT GTGGTTTTTT
 TTTTTTTTTT TTTGGTTTGT TTGTTTTTTT GGTAGGATAT GAAAGCAGGA TGCTGGGTTT
 AAAAGCAAAG CTTGAAAGTA GAGGATATAA TCTTCAGACA TAGTATATAT TATGCTAGAA
 AATCTTATAT CTGGACTGTA AATTATTCAT CTTTGTTAAT GGAAAACTTA TTTTCTACTA
 TTGCAGGGTG
 R
 AAGGTGAAGG GGAATATACT GATATCCAAG GACTAGAATG GAGTGGTAAC TTTCATTTTA
 CAGCTGCTCC AGACCTGAAA TTAAAGCTTC ACATGTAGAT GTGATGTTAA ATTAAAGTTG
 AAATGTAGTA ATTGAAGCTT TTAGTTGTAA GGAAAGCAAC TTAATCTGTT ATTTGAAATG
 ACTTCATACA CTACCCCTAT AAGTTTGCCA ATAAAACCAT CACCTGCTTA CACCTTTTTG
 AACTTTATAT

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000002 AC092833
dbSNP Blast Analysis
UniGene Cluster ID
99841

  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.
SourceA/A
A/G
G/G
HWPA
G
ss1296762630EAS 1008AF 0.001000000.99900001
EUR 1006AF 0.135199990.86479998
AFR 1322AF 0.006100000.99390000
AMR 694AF 0.086500000.91350001
SAS 978AF 0.147199990.85280001
ss166456430PGP 2IG 1.00000000 0.500000000.50000000
ss1686275507ExAc_Aggregated_Populations 25792AF 0.111662530.88833749
ss231124922pilot_1_CEU_low_coverage_panel 120AF 0.166666670.83333331
ss4337587HapMap-CEUEuropean 226IG0.017699110.300884960.681415920.438578000.168141590.83185840
HapMap-HCBAsian 90IG 0.022222220.977777781.000000000.011111110.98888886
HapMap-JPTAsian 90IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-ASW 98IG 0.081632650.918367331.000000000.040816330.95918369
HAPMAP-GIH 176IG0.022727270.261363630.715909061.000000000.153409090.84659094
HAPMAP-MEX 100IG 0.120000000.880000001.000000000.060000000.94000000
HAPMAP-TSI 176IG0.011363640.170454550.818181811.000000000.096590910.90340906
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss491782137CSAgilent 593GF0.020000000.221999990.758000020.751830000.131000000.86900002

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.213+/-0.2470000ALFRED: 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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