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Reference SNP (refSNP) Cluster Report: rs2395029                 **Clinical Channel**
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:100/151
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:G/T (FWD)
Allele Origin:
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:G=0.0283/3311 (ExAC)
G=0.0333/167 (1000 Genomes)
G=0.0290/377 (GO-ESP)
G=0.0265/3324 (TOPMED)
HGVS Names
  • CM000668.2:g.31464003T>G
  • NC_000006.11:g.31431780T>G
  • NC_000006.12:g.31464003T>G
  • NR_040662.1:n.733T>G
  • NT_113891.2:g.2941434T>G
  • NT_113891.3:g.2941328T>G
  • NT_167249.1:g.2762550T>G
  • NT_167249.2:g.2763252T>G
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 ss278726096 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs2395029 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
ss3357812TSC-CSHL|TSC1607110byFreqfwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac09/20/0110/21/04100Genomicunknown
ss5320801TSC-CSHL|TSC1608635fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac09/20/0210/10/03117Genomicunknown
ss65844405KRIBB_YJKIM|KHS20201fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac10/17/0611/15/06127Genomicunknown
ss66557192ILLUMINA|HumanHap300v1.1_rs2395029fwd/TG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac11/09/0611/09/06127Genomicunknown
ss67251545ILLUMINA|HumanHap550v1.1_rs2395029fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac11/14/0611/14/06127Genomicunknown
ss67649309ILLUMINA|HumanHap650Yv1.0_rs2395029fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac11/14/0611/14/06127Genomicunknown
ss68971560PERLEGEN|PGP04752661byFreqfwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac01/30/0708/14/07127Genomicunknown
ss70729885ILLUMINA|HumanHap550v3.0__rs2395029rev/TA/Cgtgcccattgaactacacattacagctgcccaggggaattggacagtatgtgtccagaga04/20/0703/30/08130Genomicunknown
ss71299225ILLUMINA|HumanHap650Yv3.0_rs2395029fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac04/23/0704/23/07127Genomicunknown
ss75006599ILLUMINA|ILMN_Human_1M_rs2395029fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac08/28/0708/29/07129Genomicunknown
ss79133249ILLUMINA|HumanHap300v2.0_rs2395029fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac04/18/0711/18/07130Genomicunknown
ss84045131KRIBB_YJKIM|KHS612777fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac12/04/0712/06/07130Genomicunknown
ss122024861ILLUMINA|HumanCNV370v1_C_rs2395029fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac04/14/0904/15/09131Genomicunknown
ss153909329ILLUMINA|Human610_Quadv1_B_rs2395029-128_T_R_1501723048rev/TA/Cgtgcccattgaactacacattacagctgcccaggggaattggacagtatgtgtccagaga06/18/0906/20/09131Genomicunknown
ss159387181ILLUMINA|Human660W-Quad_v1_A_rs2395029-128_T_R_1501723048rev/TA/Cgtgcccattgaactacacattacagctgcccaggggaattggacagtatgtgtccagaga07/06/0907/07/09131Genomicunknown
ss171238093ILLUMINA|HumanCNV370-Quadv3_C_rs2395029-128_T_R_1501723048rev/TA/Cgtgcccattgaactacacattacagctgcccaggggaattggacagtatgtgtccagaga10/01/0910/03/09135Genomicunknown
ss173324651ILLUMINA|Human1M-Duov3_B_rs2395029-128_T_R_1501723048rev/TA/Cgtgcccattgaactacacattacagctgcccaggggaattggacagtatgtgtccagaga10/01/0910/03/09135Genomicunknown
ss2333984231000GENOMES|pilot_1_CEU_3003052_chr6_31539759fwd/G/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac05/01/1005/01/10136Genomicunknown
ss278726096GMI|GMI_AK_SNP_3046335fwd/G/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac12/16/1012/16/10137Genomicunknown
ss342206514NHLBI-ESP|ESP2500-chr6-31431780byFreqfwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac03/25/1109/05/14136Genomicunknown
ss410922790ILLUMINA|Cardio-Metabo_Chip_11395247_A_rs2395029rev/TA/Cgtgcccattgaactacacattacagctgcccaggggaattggacagtatgtgtccagaga06/07/1106/07/11136Genomicunknown
ss479488851ILLUMINA|HumanOmni2.5-4v1_D_kgp10902-0_T_R_1804096593fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg01/30/1210/28/16137Genomicunknown
ss485227649ILLUMINA|HumanOmni2.5-4v1_B_SNP6-31539759-0_T_R_1649069565fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg01/30/1210/28/16137Genomicunknown
ss491381778EXOME_CHIP|.GWAS._98004_chr_6_31431780fwd/BG/Ttctctggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatgggcac03/05/1203/05/12137Genomicunknown
ss491885021CLINSEQ_SNP|SNV-chr6-31539759byFreqfwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg03/06/1209/05/14137Genomicunknown
ss533031097ILLUMINA|HumanOmni5-4v1_B_kgp10902-0_T_R_1804096593fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg06/22/1208/29/15146Genomicunknown
ss559113405TISHKOFF|snp_chr6_31431780fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg11/22/1211/23/12138Genomicunknown
ss653034414SSMP|6_31431780fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg12/14/1202/11/15138Genomicunknown
ss779478188ILLUMINA|HumanOmni25Exome-8v1_A_kgp10902-0_T_R_1804096593fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/30/1307/09/15146Genomicunknown
ss780683408ILLUMINA|HumanOmni25Exome-8v1_A_exm-rs2395029-131_T_R_1990490351fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/30/1307/09/15146Genomicunknown
ss780994048ILLUMINA|HumanOmni2.5-4v1_H_kgp10902-0_T_R_1804096593fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/30/1307/28/15146Genomicunknown
ss783356804ILLUMINA|HumanOmniExpressExome-8v1_A_exm-rs2395029-131_T_R_1990490351fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/31/1306/19/15146Genomicunknown
ss825463767ILLUMINA|HumanCNV370v1_C_rs2395029-117_T_R_IFB1153367755:0fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg06/24/1311/21/14144Genomicunknown
ss834948177ILLUMINA|HumanOmni2.5-8v1_A_kgp10902-0_T_R_1804096593fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg09/18/1307/28/15146Genomicunknown
ss982764853EVA-GONL|EVA-GONL_rs2395029fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg04/23/1404/24/14142Genomicunknown
ss1067477106JMKIDD_LAB|HGDP_exomes_chr6_31431780fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg07/09/1407/09/14142Genomicunknown
ss1073505076JMKIDD_LAB|HGDP_WGS_chr6_31431780fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg07/10/1407/11/14142Genomicunknown
ss13195556111000GENOMES|PHASE3_V1_31487821fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg08/16/1408/16/14142Genomicunknown
ss1397449754HAMMER_LAB|HAMMER_LAB_rs2395029fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg09/30/1409/30/14146Genomicunknown
ss1584045171EVA_FINRISK|EVA_FINRISK_rs2395029fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg02/27/1502/27/15144Genomicunknown
ss1592308880EVA_DECODE|EVA_DECODE_6_31539759_272918_rs2395029fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg03/02/1503/03/15144Genomicunknown
ss1615275939EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_6_31431780_17465250fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg03/04/1503/04/15144Genomicunknown
ss1658269972EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_6_31431780_17465250fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg03/04/1503/04/15144Genomicunknown
ss1688229396EVA_EXAC|EVA_EXAC_3250664fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg03/04/1503/04/15144Genomicunknown
ss1711120929EVA_MGP|EVA_XIMO_236689fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg03/09/1503/09/15144Genomicunknown
ss1712850830EVA_SVP|EVA_SVP_545197fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg03/12/1503/12/15144Genomicunknown
ss1752628383ILLUMINA|OmniExpressExome-8v1-1_B_exm-rs2395029-131_T_R_1990490351fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/27/1506/09/15146Genomicunknown
ss1917802355ILLUMINA|HumanExome-12v1-1_B_exm-rs2395029-131_T_R_1990490351fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg10/16/1510/16/15147Genomicunknown
ss1926017269WEILL_CORNELL_DGM|SNV:chr6:31431780fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg10/16/1510/17/15147Genomicunknown
ss1946173250ILLUMINA|HumanCoreExome-12v1-0_C_exm-rs2395029-131_T_R_1990490351fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg10/29/1510/29/15147Genomicunknown
ss1958887926ILLUMINA|exm-rs2395029-131_T_R_1990490351fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg11/13/1511/13/15147Genomicunknown
ss2094824578ILLUMINA|Immuno_BeadChip_11419691_B_rs2395029-131_T_R_1866543436fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg09/27/1609/27/16150Genomicunknown
ss2095177813ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs2395029-131_T_R_1866543436fwd/BG/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg09/27/1609/27/16150Genomicunknown
ss2151807822USC_VALOUEV|NC_000006.11:g.31431780T>Gfwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg11/17/1611/17/16150Genomicunknown
ss2282941692HUMAN_LONGEVITY|HLI-6-31464003-T-Gfwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg11/18/1611/18/16150Genomicunknown
ss2451316154TOPMED|6_31431780_T/Gfwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg11/20/1611/20/16150Genomicunknown
ss2634429445ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp10902-0_T_R_1804096593fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg02/02/1702/02/17151Genomicunknown
ss2634429446ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs2395029-131_T_R_19083506fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg02/02/1702/02/17151Genomicunknown
ss2634429447ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_seq-rs2395029-131_T_R_2130fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg02/02/1702/02/17151Genomicunknown
ss2707401445GRF|rs2395029fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg02/13/1702/13/17151Genomicunknown
ss2735646584GNOMAD|exomes_rs2395029fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/17/1705/17/17151Genomicunknown
ss2747581096GNOMAD|coding_rs2395029fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/17/1705/17/17151Genomicunknown
ss2837420187GNOMAD|rs2395029fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/18/1705/18/17151Genomicunknown
ss2985361663AFFY|Axiom_PsorMich_Affx-28456993fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/24/1705/24/17151Genomicunknown
ss2985993860AFFY|Axiom_Smokesc1_Affx-28456993fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/24/1705/24/17151Genomicunknown
ss2998794240SWEGEN|NC_000006.11:g.31431780T>Gfwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg05/30/1705/30/17151Genomicunknown
ss3022599142ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm-rs2395029-131_T_R_1990490351fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg06/28/1706/28/17151Genomicunknown
ss3493828523TOPMED|TOPMed_freeze_5?chr6:31,464,003fwd/G/Tggacacatactgtccaattcccctgggcagctgtaatgtgtagttcaatg10/05/1710/05/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs2395029|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='G/T'|mol=Genomic|build=151
 ACACAGGTAA TCTAAGGAGA GTTGATCAAG GCCGTGGAAG AGTCCTCCAG CCACTATTGG
 CCATCAAAGG AGTCCTCTGT GTCCCAGGAA TGGTCCTGCT TTGGTGTCCC TGGTGTGACC
 CATCACCCGC TGGGAACAGC CTGAGAGAAG TAGGGCCTCT GCACCAATGC TGCTGAGGAT
 GTCAGAGCAC AGGAACGAGG CCTTGGGAAA TTACCTGGAA ATGCGACTGA AATCTTCCTT
 CCTGAGGGGT CTGGGCTCTT GGAAATCAAA CCCTCTCAGG TTGGGTGGCT GGACGATTCT
 CCTCACACTT ACAATGGGAC AAGGGGAACC AGGAGGCCCC CAAGGGGATC CCTGGGTTCC
 ACACGAACTC CTCCTACCCT CATTGTGTGA CAGCAGCCAT GCCTCCTCCT GGGGATCAGG
 ATCTATTACC TGTGCCTGGA GAGGAGGGGA CTCCTCTTCT CACCCGCTGG TCTCTGGACA
 CATACTGTCC AATTCCCCTG
 K
 GGCAGCTGTA ATGTGTAGTT CAATGGGCAC TCATTTGTCC CCTTTTAAGG GTACCCTCCT
 TTAGAATCCA GGACCTTCTA CCCTGCAGAG TGTGGTTTTG GGAGAGAAGT GCAAAATCCC
 ACGACAGGTG AGTTGAAGGA ATGGGATATG GAGCCACATC CACTTCCACC CCTTGGTATC
 TGGACCCACG TGTTCTTCCT ACTGAGATTA CAGAACTGTA GAGATGTCTT TGATTTTTAA
 AATGCACCAT GTCCTGAAAG ATGGCACCCT CCCACCCGCA GAGTGCTTCC TGCAAGCTGG
 CGTTGAGCTG TGCCTATAGA AGCTCTTTTC AACATTCTTT ATGGCCAGCA GCCCTTGGTT
 GGTGCAGATG GTGATAGGAC CAGTGGGTCC CACAGCATGG CCACACTGCA CCTCCTTCGC
 TGTCAAGTGG GTCCCCCACG AAGATACTGC ACGGAGAGCA GTGCCAAGCC TGTGGATCAG
 GAATATCAAC AGCCCCCAGA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NC_000006.9
dbSNP Blast Analysis
UniGene Cluster ID
520017
OMIM
142830
604676

  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.
SourceG/G
G/T
T/T
HWPG
T
ss1319555611EAS 1008AF 0.011900000.98809999
EUR 1006AF 0.043700000.95629996
AFR 1322AF 0.004500000.99550003
AMR 694AF 0.020200000.97979999
SAS 978AF 0.093000000.90700001
ss1688229396ExAc_Aggregated_Populations121362AF 0.027479770.97252023
ss233398423pilot_1_CEU_low_coverage_panel 120AF 0.033333340.96666664
ss3357812HapMap-CEUEuropean 226IG 0.115044250.884955761.000000000.057522130.94247788
HapMap-HCBAsian 86IG 0.023255810.976744171.000000000.011627910.98837209
HapMap-JPTAsian 86IG 1.00000000 1.00000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
YRISub-Saharan African 120IG 1.00000000 1.00000000
CHBAsian 88IG 0.022727270.977272751.000000000.011363640.98863637
JPTAsian 86IG 1.00000000 1.00000000
CEUEuropean 120IG 0.100000000.899999981.000000000.050000000.94999999
HAPMAP-ASW 98IG 0.020408160.979591851.000000000.010204080.98979592
HAPMAP-CHBAsian 82IG 1.00000000 1.00000000
HAPMAP-CHD 170IG 0.023529410.976470591.000000000.011764710.98823529
HAPMAP-GIH 176IG0.011363640.329545470.659090940.250592000.176136360.82386363
HAPMAP-LWK 180IG 0.066666670.933333341.000000000.033333340.96666664
HAPMAP-MEX 100IG 0.060000000.940000001.000000000.030000000.97000003
HAPMAP-MKK 286IG0.013986010.244755240.741258740.654721000.136363640.86363637
HAPMAP-TSI 176IG 0.068181820.931818191.000000000.034090910.96590906
ENSEMBL_Watson 2IG 1.00000000 1.00000000
ss342206514ESP_Cohort_Populations 4552GF0.002196840.051405970.946397190.020022000.027899820.97210020
ss491885021CSAgilent 1323GF 0.062000000.937999961.000000000.031000000.96899998
ss65844405KHP1 180AF 1.00000000 1.00000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.055+/-0.1560000ALFRED: 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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