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Reference SNP (refSNP) Cluster Report: rs3788013                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/151
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/C (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.3964/1985 (1000 Genomes)
A=0.4462/56025 (TOPMED)
HGVS Names
  • CM000683.2:g.42421219C>A
  • NC_000021.8:g.43841328C>A
  • NC_000021.9:g.42421219C>A
  • NG_029750.1:g.22358C>A
  • NM_001001895.2:c.932+2610C>A
  • NM_001243467.1:c.932+2610C>A
  • NM_018961.3:c.1046+2610C>A
  • XR_244316.1:n.1016+2610C>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 ss283556627 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3788013 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
ss4974383YUSUKE|IMS-JST144919byFreqfwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag08/12/0210/10/03107Genomicunknown
ss10984191BCM_SSAHASNP|chr21.NT_030188.2_590654fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag06/30/0310/10/03116Genomicunknown
ss12509543WI_SSAHASNP|chr21.NT_030188.2_590654fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag07/04/0310/10/03116Genomicunknown
ss14445384WUGSC_SSAHASNP|chr21.NT_030188.3_590654byFreqfwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag11/05/0310/25/06119Genomicunknown
ss44259224ABI|hCV1724078fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag07/18/0507/18/05126Genomicunknown
ss67303215ILLUMINA|HumanHap550v1.1_rs3788013fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag11/14/0611/14/06127Genomicunknown
ss67708168ILLUMINA|HumanHap650Yv1.0_rs3788013fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag11/14/0611/14/06127Genomicunknown
ss68221684ILLUMINA|HumanHap250Sv1.0_rs3788013fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag12/06/0612/07/06127Genomicunknown
ss70781866ILLUMINA|HumanHap550v3.0__rs3788013fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag04/20/0703/30/08130Genomicunknown
ss71358356ILLUMINA|HumanHap650Yv3.0_rs3788013fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag04/23/0704/23/07127Genomicunknown
ss75916487ILLUMINA|ILMN_Human_1M_rs3788013fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag08/28/0708/29/07129Genomicunknown
ss78330902HGSV|Cor12878_SNV_20070510.chr21_42714397byFreqfwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag10/17/0709/05/14129Genomicunknown
ss78946741HGSV|Cor18507_SNV_20070510.chr21_42714397fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag10/19/0710/21/07129Genomicunknown
ss84184483KRIBB_YJKIM|KHS652841fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag12/04/0712/06/07130Genomicunknown
ss85322281HGSV|Cor19129_SNV_20070510.chr21_42714397fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag12/06/0712/09/07130Genomicunknown
ss91850991BCMHGSC_JDW|JWB-1501269fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag02/26/0803/02/08129Genomicunknown
ss96172442HUMANGENOME_JCVI|1103643127698fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag03/25/0803/25/08130Genomicunknown
ss106215396BGI|BGI_rs3788013fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag09/13/0806/18/09130Genomicunknown
ss1125058871000GENOMES|CEU.trio.12.15.2008_3774450_chr21_42714397fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag12/17/0812/17/08130Genomicunknown
ss1139513141000GENOMES|NA19240_2008_12_16_3411204_chr21_42714397fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag12/18/0812/18/08130Genomicunknown
ss117540056ILLUMINA-UK|NA18507_000046105_NCBI36.1_chr21_42714397fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag01/19/0901/19/09130Genomic99 %
ss138323081ENSEMBL|ENSSNP11893486fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag05/15/0905/17/09131Genomicunknown
ss139555618ENSEMBL|ENSSNP3462345fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag12/08/0810/16/09131Genomicunknown
ss154269365ILLUMINA|Human610_Quadv1_B_rs3788013-126_T_F_1502216375fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag06/18/0906/20/09131Genomicunknown
ss159446138ILLUMINA|Human660W-Quad_v1_A_rs3788013-126_T_F_1502216375fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag07/06/0907/07/09131Genomicunknown
ss169619877COMPLETE_GENOMICS|NA19240_36_chr21_42714397fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag10/01/0910/01/09132Genomicunknown
ss172075589COMPLETE_GENOMICS|NA20431_36_chr21_42714397fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag10/01/0910/01/09132Genomicunknown
ss173639538ILLUMINA|Human1M-Duov3_B_rs3788013-126_T_F_1502216375fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag10/01/0910/04/09132Genomicunknown
ss204029514BUSHMAN|BUSHMAN-chr21-42714396fwd/TA/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag02/16/1003/10/10132Genomicunknown
ss2285865771000GENOMES|pilot_1_YRI_10396260_chr21_42714397fwd/A/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag04/22/1004/22/10132Genomicunknown
ss2379983621000GENOMES|pilot_1_CEU_7602991_chr21_42714397fwd/A/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag05/01/1005/01/10132Genomicunknown
ss2441337111000GENOMES|pilot_1_CHB+JPT_6018788_chr21_42714397fwd/A/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag05/01/1005/01/10132Genomicunknown
ss283556627GMI|GMI_AK_SNP_7877048fwd/A/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag12/16/1012/16/10137Genomicunknown
ss287538162GMI|GMI_NA10851_SNP_3550953fwd/A/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag12/17/1012/17/10138Genomicunknown
ss292718184PJP|SNP_2224542_chr21_42714397fwd/A/Cgagaaaagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtgtcaag01/21/1101/21/11134Genomicunknown
ss566521787TISHKOFF|snp_chr21_43841328fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg11/22/1211/23/12138Genomicunknown
ss662432642SSMP|21_43841328fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg12/14/1202/14/15138Genomicunknown
ss995158377EVA-GONL|EVA-GONL_rs3788013fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg04/23/1405/01/14142Genomicunknown
ss1082530174JMKIDD_LAB|HGDP_WGS_chr21_43841328fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg07/10/1407/12/14142Genomicunknown
ss13664345731000GENOMES|PHASE3_V1_80295008fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg08/16/1408/16/14142Genomicunknown
ss1429196820DDI|DDI_rs3788013fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg11/04/1411/04/14144Genomicunknown
ss1579679199EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3788013fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg02/19/1502/20/15144Genomicunknown
ss1639641573EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_21_43841328_44257327fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg03/04/1503/04/15144Genomicunknown
ss1682635606EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_21_43841328_44257327fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg03/04/1503/04/15144Genomicunknown
ss1699230013EVA_DECODE|EVA_DECODE_21_42714397_250063_rs3788013fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg03/02/1503/05/15144Genomicunknown
ss1713726896EVA_SVP|EVA_SVP_1420975fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg03/12/1503/12/15144Genomicunknown
ss1809705699HAMMER_LAB|Hsieh_8737323fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg07/15/1507/16/15146Genomicunknown
ss1938708884WEILL_CORNELL_DGM|SNV:chr21:43841328fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg10/16/1510/19/15147Genomicunknown
ss1946570338ILLUMINA|HumanCoreExome-12v1-0_C_rs3788013-131_T_F_1889765586fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg10/29/1510/29/15147Genomicunknown
ss1959957376ILLUMINA|rs3788013-131_T_F_1889765586fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg11/13/1511/13/15147Genomicunknown
ss1969234742GENOMED|rs3788013fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg02/16/1602/16/16147Genomicunknown
ss2030128887JJLAB|SNP10631442fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg08/29/1608/31/16149Genomicunknown
ss2094921355ILLUMINA|Immuno_BeadChip_11419691_B_imm_21_42714397-1_T_F_1670108748fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg09/27/1609/27/16150Genomicunknown
ss2095120038ILLUMINA|InfiniumImmunoArray-24v2-0_A_imm_21_42714397-1_T_F_2310574522fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg09/27/1609/27/16150Genomicunknown
ss2095120039ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs3788013-138_T_F_2264012458fwd/TA/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg09/27/1609/27/16150Genomicunknown
ss2158733852USC_VALOUEV|NC_000021.8:g.43841328C>Afwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg11/17/1611/17/16150Genomicunknown
ss2246075147HUMAN_LONGEVITY|HLI-21-42421219-C-Afwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg11/18/1611/18/16150Genomicunknown
ss2412765862TOPMED|21_43841328_C/Afwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg11/19/1611/19/16150Genomicunknown
ss2629563650SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV6782037fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg01/06/1701/06/17151Genomicunknown
ss2704465137GRF|rs3788013fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg02/13/1702/13/17151Genomicunknown
ss2710951378ILLUMINA|Consortium-OncoArray_15047405_A_rs3788013-131_T_F_1889765586fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg03/22/1703/22/17151Genomicunknown
ss2972195251GNOMAD|rs3788013fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg05/23/1705/23/17151Genomicunknown
ss2985849410AFFY|Axiom_Smokesc1_Affx-18083115fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg05/24/1705/24/17151Genomicunknown
ss3018952705SWEGEN|NC_000021.8:g.43841328C>Afwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg05/30/1705/30/17151Genomicunknown
ss3022163454ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs3788013-138_T_F_2264012458fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg06/28/1706/28/17151Genomicunknown
ss3028904171BIOINF_KMB_FNS_UNIBA|21.42421219C>Afwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg07/05/1707/05/17151Genomicunknown
ss3352737830CSHL|rs3788013fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg10/02/1710/02/17151Genomicunknown
ss3371684955TOPMED|TOPMed_freeze_5?chr21:42,421,219fwd/A/Caagctgctcagcctcatgggtgtgctgttggggtggagctcttgcaggtg10/03/1710/03/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3788013|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C'|mol=Genomic|build=151
 TCACAGACAC AGCTGCTATT GAAGTCTCTG AGTGTGAGGA AAGCCTAAGT TTTTAAAAAA
 AAATGCCTTC CAACTGCATA AGTCAGACCT GCTCAGAATA ACCTTGCTTT TGATTAATTT
 AAGCTCAACT GATTAGGGGT TCTAGTCACA TTTGTAAAAT CTCCTTCCAG CAGCACCTAG
 ACTAGCATTT GATGGGATAG CTAGGAAGGC TGTGTGTGAT GCTTAGGATG GCTACTGCCT
 CCCTTCCATC CTCCAGCTCT CATGAGAATG CCTCTTGTAG CCCACCCTGA TCAGACATGT
 GCTAAAAAGG AAGTCTAGGA ACTGTCGTTC AGTCTGGCCA AGTTGCCACA CCATAAAGCC
 ATTGCAAAGT GTTAAGGTGG CTCTTGTGAG CTTTTTCACT CTCTTCTCCC AGGTTCCAGT
 TAGGAGAGTG GAGAGAGCAG GCAGAGGTCA GAGTACACAT GGTGAAAAAA GAGAAAAGCT
 GCTCAGCCTC ATGGGTGTGC
 M
 TGTTGGGGTG GAGCTCTTGC AGGTGTCAAG ACTGATGGTT GGAACAACTG AATGATGAGA
 GTGGGAGGAG AAGGGCAGAA ATACACAGAA AAACCCTATG TTGTGGTTCT GGGCTTCCTG
 GCACCTTCAG AGCTGTGTGG CTGGGGAAGA GAGCCTGGAA AAACACCATC GTGGCCATCC
 CTCTGTCTCC AGGCAGGAGG TCTTAAAACC ATTTTATATT TCACTCATTT GTTTAATTCT
 CTCCTAAAAT GCTCCACAGC TTCTCTAGGG TTCCCCTCAC CACCCTGACA AATAAATAAA
 TCATTAAGTT GAACACAGAT GTATCAGCAT CTACTCAATC TATAGATTTT CAGATCTGTG
 CTGGACATTT GCTGTGGACT TCTATTTCCA GCATCTATAC ATCCAGGGAA TTATTTTCTG
 TACCCTTCCT AATGAGATTC ATGCACATGG CAAAACTATG AAAATTGTGA CGTTTTATTT
 GAGTAGTCAT TAAAAGCTGC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_030188 ABBA01004544
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.
SourceA/A
A/C
C/C
HWPA
C
ss117540056YRI 2IG1.00000000 1.00000000
ss1366434573EAS 1008AF 0.294599980.70539999
EUR 1006AF 0.387700020.61230004
AFR 1322AF 0.552999970.44700003
AMR 694AF 0.389000000.61100000
SAS 978AF 0.303699970.69629997
ss138323081ENSEMBL_Watson 2IG 1.00000000 0.500000000.50000000
ss139555618ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss169619877YRISub-Saharan African 2IG 1.00000000 0.500000000.50000000
ss172075589PGP 2IG 1.00000000 0.500000000.50000000
ss228586577pilot_1_YRI_low_coverage_panel 118AF 0.610169470.38983050
ss237998362pilot_1_CEU_low_coverage_panel 120AF 0.349999990.64999998
ss244133711pilot_1_CHB+JPT_low_coverage_panel 120AF 0.341666670.65833336
ss4974383JBIC-allele 1452AF 0.327899990.67210001
ss78330902HapMap-CEUEuropean 224IG0.125000000.526785730.348214300.250592000.388392870.61160713
HapMap-HCBAsian 86IG0.046511630.441860470.511627910.402784000.267441870.73255813
HapMap-JPTAsian 170IG0.200000000.364705890.435294120.050043000.382352950.61764705
HapMap-YRISub-Saharan African 226IG0.309734520.522123870.168141590.527089000.570796490.42920354
HAPMAP-ASW 98IG0.244897960.469387770.285714300.751830000.479591850.52040815
HAPMAP-CHBAsian 82IG0.073170730.463414640.463414640.583882000.304878060.69512194
HAPMAP-CHD 170IG0.058823530.482352940.458823530.200325000.300000010.69999999
HAPMAP-GIH 176IG0.090909090.465909090.443181810.583882000.323863630.67613637
HAPMAP-LWK 180IG0.255555570.455555560.288888900.438578000.483333320.51666665
HAPMAP-MEX 100IG0.140000000.500000000.360000010.751830000.389999990.61000001
HAPMAP-MKK 286IG0.244755240.503496530.251748261.000000000.496503500.50349653
HAPMAP-TSI 176IG0.147727270.568181810.284090910.150222000.431818190.56818181
ss96172442J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.479+/-0.1010000ALFRED: 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_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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