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Reference SNP (refSNP) Cluster Report: rs3758391                 
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
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:C=0.4942/2475 (1000 Genomes)
T=0.3863/48513 (TOPMED)
HGVS Names
  • CM000672.2:g.67883584T>C
  • NC_000010.10:g.69643342T>C
  • NC_000010.11:g.67883584T>C
  • NG_047020.1:g.1718T>C
  • NG_050664.1:g.3923T>C
  • NM_001142498.1:c.-2029T>C
  • NM_012238.4:c.-1138T>C
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 ss280661954 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3758391 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
ss4944423YUSUKE|IMS-JST111687byFreqfwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga08/01/0210/10/03107Genomicunknown
ss10642345BCM_SSAHASNP|chr10.NT_008583.15_18194490fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga06/29/0310/10/03116Genomicunknown
ss12115362WI_SSAHASNP|chr10.NT_008583.15_18194490fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga07/04/0310/10/03116Genomicunknown
ss15870153SC_SNP|NT_008583.16_18194497fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga11/17/0311/22/03120Genomicunknown
ss38584584ABI|hCV3003909byFreqfwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga07/15/0511/02/06126Genomicunknown
ss46548786PERLEGEN|PS02264202fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga08/01/0508/01/05126Genomicunknown
ss65776782ILLUMINA|Human1-rs3758391fwd/TC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga10/10/0610/10/06127Genomicunknown
ss75007261ILLUMINA|ILMN_Human_1M_rs3758391fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga08/28/0708/29/07129Genomicunknown
ss79745443HGSV|Cor18507_SNV_20070510.chr10_69313348fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga11/23/0711/23/07130Genomicunknown
ss83362900HGSV|Cor19240_SNV_20070510.chr10_69313348fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga11/30/0712/04/07130Genomicunknown
ss88254589BCMHGSC_JDW|JWB-0296345fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga02/26/0802/27/08129Genomicunknown
ss97659250HUMANGENOME_JCVI|1103649968581fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga03/29/0803/29/08130Genomicunknown
ss1095331201000GENOMES|CEU.trio.12.15.2008_2374296_chr10_69313348fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga12/16/0812/16/08130Genomicunknown
ss1134179221000GENOMES|NA19240_2008_12_16_2143675_chr10_69313348fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga12/18/0812/18/08130Genomicunknown
ss119210797ILLUMINA-UK|NA18507_000090457_NCBI36.1_chr10_69313348fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga01/21/0901/22/09130Genomic99 %
ss119460499KRIBB_YJKIM|KHS1622746fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga02/04/0902/04/09131Genomicunknown
ss131930199ENSEMBL|ENSSNP6746045fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga05/11/0905/13/09131Genomicunknown
ss143099553ENSEMBL|ENSSNP8274505fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga12/08/0810/19/09131Genomicunknown
ss160637551ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3758391-128_T_R_1513976407rev/TA/Gtctaatcttaactaaggacccatataaccctggtagatctagagccagtgtttgttatgg08/04/0910/04/09131Genomicunknown
ss168510515COMPLETE_GENOMICS|NA07022_36_chr10_69313348fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga09/30/0910/01/09132Genomicunknown
ss170316642COMPLETE_GENOMICS|NA19240_36_chr10_69313348fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga10/01/0910/04/09132Genomicunknown
ss173626897ILLUMINA|Human1M-Duov3_B_rs3758391-128_T_R_1513976407rev/TA/Gtctaatcttaactaaggacccatataaccctggtagatctagagccagtgtttgttatgg10/01/0910/04/09132Genomicunknown
ss174603808COMPLETE_GENOMICS|NA20431_36_chr10_69313348fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga10/01/0910/04/09132Genomicunknown
ss201657554BUSHMAN|BUSHMAN-chr10-69313347fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga02/16/1003/08/10132Genomicunknown
ss207397730BCM-HGSC-SUB|BCM_CMT_1011-2089243fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga03/15/1003/18/10132Genomicunknown
ss2247862141000GENOMES|pilot_1_YRI_6595897_chr10_69313348fwd/C/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga04/22/1004/22/10132Genomicunknown
ss2352206671000GENOMES|pilot_1_CEU_4825296_chr10_69313348fwd/C/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga05/01/1005/01/10132Genomicunknown
ss2419178141000GENOMES|pilot_1_CHB+JPT_3802891_chr10_69313348fwd/C/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga05/01/1005/01/10132Genomicunknown
ss254396353BL|SNP84997_10_69313348fwd/BC/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga08/19/1008/19/10134Genomicunknown
ss280661954GMI|GMI_AK_SNP_4982289fwd/C/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga12/16/1012/16/10137Genomicunknown
ss286211364GMI|GMI_NA10851_SNP_2224149fwd/C/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga12/17/1012/17/10138Genomicunknown
ss290862088PJP|SNP_368446_chr10_69313348fwd/C/Tccataacaaacactggctctagatctaccagggttatatgggtccttagttaagattaga01/21/1101/21/11134Genomicunknown
ss480819455ILLUMINA|HumanOmni2.5-4v1_B_rs3758391-128_T_R_1615265698fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga01/30/1210/28/16137Genomicunknown
ss480835129ILLUMINA|HumanOmniExpress-12v1_C_rs3758391-131_T_R_1857479423fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga01/30/1210/27/16137Genomicunknown
ss481764993ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3758391-131_T_R_1865157865fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga01/30/1208/28/15146Genomicunknown
ss485204571ILLUMINA|HumanOmni2.5-4v1_D_rs3758391-131_T_R_1857479423fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga01/30/1210/27/16137Genomicunknown
ss537189627ILLUMINA|HumanOmni5-4v1_B_rs3758391-131_T_R_1889635996fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga06/22/1208/29/15146Genomicunknown
ss562024213TISHKOFF|snp_chr10_69643342fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga11/22/1211/23/12138Genomicunknown
ss656904486SSMP|10_69643342fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga12/14/1202/12/15138Genomicunknown
ss778894942ILLUMINA|HumanOmni25Exome-8v1_A_rs3758391-131_T_R_1865157865fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga05/30/1307/10/15146Genomicunknown
ss783048255ILLUMINA|HumanOmni2.5-4v1_H_rs3758391-131_T_R_1857479423fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga05/30/1307/29/15146Genomicunknown
ss784006934ILLUMINA|HumanOmniExpressExome-8v1_A_rs3758391-131_T_R_1889635996fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga05/31/1306/18/15146Genomicunknown
ss832306057ILLUMINA|HumanOmniExpress-12v1_H_rs3758391-131_T_R_1857479423fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga09/17/1306/18/15146Genomicunknown
ss834356124ILLUMINA|HumanOmni2.5-8v1_A_rs3758391-131_T_R_1865157865fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga09/18/1307/29/15146Genomicunknown
ss987604788EVA-GONL|EVA-GONL_rs3758391fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga04/23/1404/25/14142Genomicunknown
ss1077074120JMKIDD_LAB|HGDP_WGS_chr10_69643342fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga07/10/1407/11/14142Genomicunknown
ss13378711741000GENOMES|PHASE3_V1_50542621fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga08/16/1408/16/14142Genomicunknown
ss1426355753DDI|DDI_rs3758391fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga11/04/1411/04/14144Genomicunknown
ss1575187137EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3758391fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga02/19/1502/19/15144Genomicunknown
ss1597275138EVA_DECODE|EVA_DECODE_10_69313348_531123_rs3758391fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga03/02/1503/03/15144Genomicunknown
ss1624794991EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_10_69643342_27904830fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga03/04/1503/04/15144Genomicunknown
ss1667789024EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_10_69643342_27904830fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga03/04/1503/04/15144Genomicunknown
ss1713187675EVA_SVP|EVA_SVP_882042fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga03/12/1503/12/15144Genomicunknown
ss1751977213ILLUMINA|OmniExpressExome-8v1-1_B_rs3758391-131_T_R_2087478520fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga05/27/1506/09/15146Genomicunknown
ss1806439283HAMMER_LAB|Hsieh_5457518fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga07/15/1507/16/15146Genomicunknown
ss1930968571WEILL_CORNELL_DGM|SNV:chr10:69643342fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga10/16/1510/17/15147Genomicunknown
ss1946284483ILLUMINA|HumanCoreExome-12v1-0_C_rs3758391-131_T_R_2087478520fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga10/29/1510/29/15147Genomicunknown
ss1959269808ILLUMINA|rs3758391-131_T_R_1889635996fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga11/13/1511/13/15147Genomicunknown
ss1967156413GENOMED|rs3758391fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga02/16/1602/16/16147Genomicunknown
ss2026210363JJLAB|SNP6712918fwd/BC/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga08/29/1608/30/16149Genomicunknown
ss2154483476USC_VALOUEV|NC_000010.10:g.69643342T>Cfwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga11/17/1611/17/16150Genomicunknown
ss2175637810HUMAN_LONGEVITY|HLI-10-67883584-T-Cfwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga11/18/1611/18/16150Genomicunknown
ss2338676913TOPMED|10_69643342_T/Cfwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga11/19/1611/19/16150Genomicunknown
ss2627575195SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV4257045fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga01/06/1701/06/17151Genomicunknown
ss2632723796ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs3758391-131_T_R_20874785fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga02/02/1702/02/17151Genomicunknown
ss2698728507GRF|rs3758391fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga02/13/1702/13/17151Genomicunknown
ss2710712699ILLUMINA|Consortium-OncoArray_15047405_A_rs3758391-131_T_R_2087478520fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga03/22/1703/22/17151Genomicunknown
ss2889997869GNOMAD|rs3758391fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga05/19/1705/19/17151Genomicunknown
ss3006655962SWEGEN|NC_000010.10:g.69643342T>Cfwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga05/30/1705/30/17151Genomicunknown
ss3021248127ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs3758391-138_T_R_2264369436fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga06/28/1706/28/17151Genomicunknown
ss3026896286BIOINF_KMB_FNS_UNIBA|10.67883584T>Cfwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga07/05/1707/05/17151Genomicunknown
ss3122637358TOPMED|TOPMed_freeze_5?chr10:67,883,584fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga09/29/1709/29/17151Genomicunknown
ss3349175019CSHL|rs3758391fwd/C/Tacaaacactggctctagatctaccagggttatatgggtccttagttaaga10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3758391|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 GAGACGGGGT TTCTCCATGT TGGTCAGGCT GGTCTCGAAC TTCCGACTTC AGGTGATCTG
 TCCGCCTCGG CCTCCCAAAG TGCTGGGATT ACAGGCAGCA GCCACCGCGC CCAGCCAGGT
 TTTAAGTCCC GCATGCATTA GCTATTTGTC CTAATGCTCT CCCTCCCCTT GACCCCCACG
 CAACCAAAGA TGGTTTTAAG GCTTCTAGGA CTGGAGATGA TTACTTTCAG AAATGAATAG
 TGGTGACCAG ATGAAATAAG ACTTTTGGAT GTAGATAGGA CCTTAGCGAT ATATTTCCAG
 CTTTTTATTT TTTATTTTAA GGATGAAGAA ACAGCTTTAA GTTGGTTGCC TAAAGTCACG
 CAGGTAATTG ATGCAGTATG GCCAGAACCC ATACTAGGCT TAAGGGACAG TGTACCATAA
 ACTCGTAGAG GTCCTTTAAA CAGATAGAAA CGCTGTGCTC CAGGCAGATG CCATAACAAA
 CACTGGCTCT AGATCTACCA
 Y
 GGGTTATATG GGTCCTTAGT TAAGATTAGA TATGGAGTCA CAGTGTGCCA GAATTTCAGG
 GAGAGAGGAA AGTGGAAGGG CTTTCCACTA AGCCTTTTGA ACTACTAGGT ACCCCTCGTT
 TTACATCTGG TTATCTCATT TAAATCTATG ACGTTTTAAA ATACTTATTA CCATTTAAGA
 CATGAGAAAA ATTAAGTTTA GAAACGGCTA GATAGCTCAC GCTAGAAAGG AAGGACTCCA
 AATTTTAACC AAGGGCAGAT GTGCATGGAG GCCAAGTCAT TTCCTTCCCA TGCTCTCATA
 CTGACCCAAC AAACCCATTC TGCACGTGAG AAAACTGAGG CCCGGAGGAG GGAATTCACA
 CACGTTTGAA GCCAAGCTGG GGCCAGAAAG TAGATCGGCT GATCTCCAAA CCTCCACGTC
 AAAGGTCTTC CCAGGAGGAC ATATGCCTTC AAGGATTTTA CAATGTATAC CACCCTACAA
 GTGATGGGAG AGAGGGGAAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_008635.1 ABBA01019551
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/T
T/T
HWPC
T
ss119210797YRI 2IG 1.00000000 0.500000000.50000000
ss131930199ENSEMBL_Watson 2IG1.00000000 1.00000000
ss1337871174EAS 1008AF 0.157699990.84230000
EUR 1006AF 0.667000000.33299997
AFR 1322AF 0.646000030.35400000
AMR 694AF 0.534599960.46540001
SAS 978AF 0.429400000.57060003
ss143099553ENSEMBL_Venter 2IG 1.00000000 0.500000000.50000000
ss168510515CEUEuropean 2IG1.00000000 1.00000000
ss170316642YRISub-Saharan African 2IG1.00000000 1.00000000
ss174603808PGP 2IG1.00000000 1.00000000
ss201657554BANTU 2IG 1.00000000 0.500000000.50000000
ss224786214pilot_1_YRI_low_coverage_panel 118AF 0.669491530.33050847
ss235220667pilot_1_CEU_low_coverage_panel 120AF 0.691666660.30833334
ss241917814pilot_1_CHB+JPT_low_coverage_panel 120AF 0.175000000.82499999
ss38584584INDIAN 850AF0.259999990.460000010.280000000.150222000.490000010.50999999
HapMap-CEUEuropean 226IG0.548672560.362831860.088495570.402784000.730088470.26991150
HapMap-HCBAsian 86IG0.023255810.255813960.720930221.000000000.151162790.84883720
HapMap-JPTAsian 172IG 0.372093020.627906980.250592000.186046510.81395346
HapMap-YRISub-Saharan African 226IG0.451327440.477876100.070796460.250592000.690265480.30973452
AoD_African_American 90AF 0.649999980.34999999
AoD_Caucasian 92AF 0.709999980.28999999
AoD_Chinese 90AF 0.230000000.76999992
AoD_Japanese 90AF 0.180000010.82000005
HAPMAP-ASW 98IG0.408163280.469387770.122448981.000000000.642857130.35714287
HAPMAP-CHBAsian 82IG 0.390243890.609756110.371093000.195121940.80487806
HAPMAP-CHD 170IG0.011764710.258823540.729411780.583882000.141176480.85882354
HAPMAP-GIH 176IG0.181818190.477272720.340909091.000000000.420454530.57954544
HAPMAP-LWK 180IG0.444444450.444444450.111111111.000000000.666666690.33333334
HAPMAP-MEX 100IG0.220000000.419999990.360000010.317310000.430000010.56999999
HAPMAP-MKK 286IG0.468531460.433566420.097902101.000000000.685314710.31468531
HAPMAP-TSI 176IG0.465909090.465909090.068181820.317310000.698863630.30113637
ss4944423JBIC-allele 898AF 0.158999990.84100002
ss97659250J. Craig Venter 2IG 1.00000000 0.500000000.50000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.500+/-0.0060000

  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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