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Reference SNP (refSNP) Cluster Report: rs3827760                 ** With other allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:107/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Association:NHGRI GWAS
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:C:germline
T:germline
Ancestral Allele:T
Variation Viewer:link to VariationViewer
Clinical Significance:With other allele [ClinVar]
MAF/MinorAlleleCount:G=0.1300/15608 (ExAC)
G=0.2356/1180 (1000 Genomes)
G=0.0104/135 (GO-ESP)
G=0.1041/13072 (TOPMED)
HGVS Names
  • CM000664.2:g.108897145A>G
  • NC_000002.11:g.109513601A>G
  • NC_000002.12:g.108897145A>G
  • NG_008257.1:g.97228T>C
  • NM_022336.3:c.1109T>C
  • NP_071731.1:p.Val370Ala
  • XP_006712267.1:p.Val402Ala
  • XP_011508804.2:p.Val450Ala
  • XP_011508805.2:p.Val418Ala
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 ss276615531 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs3827760 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
ss5014251YUSUKE|IMS-JST189188byFreqfwd/BC/Ttcagctccacgtacaactctgagaaggctgtgtgaaaacgtggcgccacctcgccgagag08/12/0210/10/03107Genomicunknown
ss20093966CSHL-HAPMAP|CSHL-HuFF-200402.chr2.NT_022171.13_11579625rev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga02/21/0403/04/04120Genomicunknown
ss21741902SSAHASNP|WGSA-200403-chr2.chr2.NT_022171.13_11579625rev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga03/20/0403/20/04121Genomicunknown
ss23670642PERLEGEN|afd4229911byFreqrev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga08/10/0409/13/04123Genomicunknown
ss44354834ABI|hCV27497202byFreqrev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga07/18/0511/03/06126Genomicunknown
ss65728092ILLUMINA|Human1-rs3827760fwd/BC/Ttcagctccacgtacaactctgagaaggctgtgtgaaaacgtggcgccacctcgccgagag10/10/0610/10/06127Genomicunknown
ss68824175PERLEGEN|PGP04229911byFreqrev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga01/30/0703/31/08127Genomicunknown
ss74807166AFFY|SNP_M-177880fwd/BC/Ttcagctccacgtacaactctgagaaggctgtgtgaaaacgtggcgccacctcgccgagag08/09/0708/09/07128Genomicunknown
ss74885862ILLUMINA|ILMN_Human_1M_rs3827760fwd/BC/Ttcagctccacgtacaactctgagaaggctgtgtgaaaacgtggcgccacctcgccgagag08/28/0708/29/07129Genomicunknown
ss80766809KRIBB_YJKIM|KHS1009056byFreqfwd/BC/Ttcagctccacgtacaactctgagaaggctgtgtgaaaacgtggcgccacctcgccgagag11/26/0709/05/14130Genomicunknown
ss106109500BGI|BGI_rs3827760rev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga09/13/0806/18/09130Genomicunknown
ss119466436KRIBB_YJKIM|KHS1628683fwd/BC/Ttcagctccacgtacaactctgagaaggctgtgtgaaaacgtggcgccacctcgccgagag02/04/0902/04/09131Genomicunknown
ss157486331GMI|GMI_SNP_76223618rev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga06/24/0906/25/09131Genomicunknown
ss159702572SEATTLESEQ|EDAR-108880033rev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga07/10/0907/10/09131Genomicunknown
ss160648840ILLUMINA|HumanOmni1-Quad_v1-0_B_rs3827760-128_B_F_1513902718fwd/BC/Ttcagctccacgtacaactctgagaaggctgtgtgaaaacgtggcgccacctcgccgagag08/04/0910/04/09131Genomicunknown
ss161166590ENSEMBL|ENSSNP1575722rev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga09/24/0909/24/09131Genomicunknown
ss173657549ILLUMINA|Human1M-Duov3_B_rs3827760-128_B_F_1513902718fwd/BC/Ttcagctccacgtacaactctgagaaggctgtgtgaaaacgtggcgccacctcgccgagag10/01/0910/04/09132Genomicunknown
ss2388263301000GENOMES|pilot_1_CHB+JPT_711407_chr2_108880033rev/A/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga05/01/1005/01/10132Genomicunknown
ss262861532OMIM-CURATED-RECORDS|12373fwd/BC/Ttcagctccacgtacaactctgagaaggctgtgtgaaaacgtggcgccacctcgccgagag09/23/1009/23/10133Genomicunknown
ss276615531GMI|GMI_AK_SNP_935740rev/A/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga12/16/1012/16/10137Genomicunknown
ss342074042NHLBI-ESP|ESP2500-chr2-109513601byFreqrev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga03/25/1109/05/14134Genomicunknown
ss480595567ILLUMINA|HumanOmni2.5-4v1_D_kgp14454942-0_B_R_1832553645rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga01/30/1210/28/16137Genomicunknown
ss480855406ILLUMINA|HumanOmni2.5-4v1_B_rs3827760-128_B_F_1735650989rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga01/30/1210/28/16137Genomicunknown
ss480873495ILLUMINA|HumanOmniExpress-12v1_C_rs3827760-131_B_F_1857505528rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga01/30/1210/27/16137Genomicunknown
ss481810006ILLUMINA|HumanOmni1-Quad_v1-0_C_rs3827760-131_B_F_1865356174rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga01/30/1208/28/15146Genomicunknown
ss483878341ILLUMINA|HumanOmni2.5-4v1_B_SNP2-108880033-0_B_R_1635302826rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga01/30/1210/28/16137Genomicunknown
ss485222694ILLUMINA|HumanOmni2.5-4v1_D_rs3827760-131_B_F_1857505528rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga01/30/1210/28/16137Genomicunknown
ss4898284831000GENOMES|20110521_exome_347732_chr2_109513601rev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga02/10/1202/21/12137Genomicunknown
ss491323037EXOME_CHIP|nonsyn_39264_chr_2_109513601rev/TA/Gctctcggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtggagctga03/05/1203/05/12137Genomicunknown
ss491789456CLINSEQ_SNP|SNV-chr2-108880033byFreqrev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga03/06/1209/05/14137Genomicunknown
ss533833996ILLUMINA|HumanOmni5-4v1_B_kgp14454942-0_B_R_1832553645rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga06/22/1208/28/15146Genomicunknown
ss649400613SSMP|2_109513601rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga12/14/1202/10/15138Genomicunknown
ss779085271ILLUMINA|HumanOmni25Exome-8v1_A_kgp14454942-0_B_R_1832553645rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/30/1307/09/15146Genomicunknown
ss781270206ILLUMINA|HumanOmni2.5-4v1_H_kgp14454942-0_B_R_1832553645rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/30/1307/28/15146Genomicunknown
ss783057297ILLUMINA|HumanOmni2.5-4v1_H_rs3827760-131_B_F_1857505528rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/30/1307/28/15146Genomicunknown
ss783466647ILLUMINA|HumanOmniExpressExome-8v1_A_exm219908-0_B_R_1918950510rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/31/1306/19/15146Genomicunknown
ss832315211ILLUMINA|HumanOmniExpress-12v1_H_rs3827760-131_B_F_1857505528rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga09/17/1306/18/15146Genomicunknown
ss834549065ILLUMINA|HumanOmni2.5-8v1_A_kgp14454942-0_B_R_1832553645rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga09/18/1307/28/15146Genomicunknown
ss977203739EVA-GONL|EVA-GONL_rs3827760rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga04/23/1404/23/14142Genomicunknown
ss1067440084JMKIDD_LAB|HGDP_exomes_chr2_109513601rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga07/09/1407/09/14142Genomicunknown
ss1069382060JMKIDD_LAB|HGDP_WGS_chr2_109513601rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga07/10/1407/10/14142Genomicunknown
ss12987100381000GENOMES|PHASE3_V1_9754503rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga08/16/1408/16/14142Genomicunknown
ss1397301346HAMMER_LAB|HAMMER_LAB_rs3827760rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga09/30/1409/30/14146Genomicunknown
ss1579023383EVA_GENOME_DK|EVA_GENOME_DK_snv_rs3827760rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga02/19/1502/20/15144Genomicunknown
ss1584020330EVA_FINRISK|EVA_FINRISK_rs3827760rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga02/27/1502/27/15144Genomicunknown
ss1586628110EVA_DECODE|EVA_DECODE_2_108880033_830016_rs3827760rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga03/02/1503/02/15144Genomicunknown
ss1604256322EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_2_109513601_5358092rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga03/04/1503/04/15144Genomicunknown
ss1647250355EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_2_109513601_5358092rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga03/04/1503/04/15144Genomicunknown
ss1686464506EVA_EXAC|EVA_EXAC_1343662rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga03/04/1503/04/15144Genomicunknown
ss1712480036EVA_SVP|EVA_SVP_174588rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga03/12/1503/12/15144Genomicunknown
ss1752304497ILLUMINA|OmniExpressExome-8v1-1_B_exm219908-0_B_R_1918950510rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/27/1506/09/15146Genomicunknown
ss1752304498ILLUMINA|OmniExpressExome-8v1-1_B_rs3827760-131_B_F_1889526853rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/27/1506/09/15146Genomicunknown
ss1917752660ILLUMINA|HumanExome-12v1-1_B_exm219908-0_B_R_1918950510rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga10/16/1510/16/15147Genomicunknown
ss1920447753WEILL_CORNELL_DGM|SNV:chr2:109513601rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga10/16/1510/16/15147Genomicunknown
ss1958447283ILLUMINA|exm219908-0_B_R_1918950510rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga11/13/1511/13/15147Genomicunknown
ss1968851959GENOMED|rs3827760rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga02/16/1602/16/16147Genomicunknown
ss2020753982JJLAB|SNP1256537rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga08/29/1608/30/16149Genomicunknown
ss2095099723ILLUMINA|InfiniumImmunoArray-24v2-0_A_rs3827760-138_B_F_2258074669rev/TA/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga09/27/1609/27/16150Genomicunknown
ss2148809672USC_VALOUEV|NC_000002.11:g.109513601A>Grev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga11/17/1611/17/16150Genomicunknown
ss2233146026HUMAN_LONGEVITY|HLI-2-108897145-A-Grev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga11/18/1611/18/16150Genomicunknown
ss2399348283TOPMED|2_109513601_A/Grev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga11/19/1611/19/16150Genomicunknown
ss2624882922SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV789654rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga01/06/1701/06/17151Genomicunknown
ss2633656104ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_kgp14454942-0_B_R_18325536rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga02/02/1702/02/17151Genomicunknown
ss2633656105ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs3827760-131_B_F_18895268rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga02/02/1702/02/17151Genomicunknown
ss2703416175GRF|rs3827760rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga02/13/1702/13/17151Genomicunknown
ss2732907347GNOMAD|exomes_rs3827760rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/17/1705/17/17151Genomicunknown
ss2746754639GNOMAD|coding_rs3827760rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/17/1705/17/17151Genomicunknown
ss2777856258GNOMAD|rs3827760rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/17/1705/17/17151Genomicunknown
ss2985181809AFFY|Axiom_PsorMich_Affx-17222553rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/24/1705/24/17151Genomicunknown
ss2990156710SWEGEN|NC_000002.11:g.109513601A>Grev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga05/30/1705/30/17151Genomicunknown
ss3022003363ILLUMINA|MEGA_Consortium_v2_15070954_A2_exm219908-0_B_R_1918950510rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga06/28/1706/28/17151Genomicunknown
ss3318870847TOPMED|TOPMed_freeze_5?chr2:108,897,145rev/A/Gggcgaggtggcgccacgttttcacacagccttctcagagttgtacgtgga10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs3827760|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 AAGTTGACTA CTGTTCCCTA AAGAGACATG ACACTGTCCC TTTGAACCCC TCCTCAGCCC
 AGCCCCATGG GAGACAGGGT TACCCAACTA AGGATAACTT GTCTTGAAGT CTTTGAGAAC
 TGCTAAAAAT GGTCATGAGG GAATTATTAT CATTGTCAAT ATAGCAGTCA TTTTCCTAGT
 GGGGAAGGGG CTATTACCGG GGTCAGGGTA CATGCACAGC CCTCTCTTGT GGCTGGCAGC
 GTTCTAGGTG TCGTTTGCCT TAAGTTATGC ATTTGTTTTA GGTGGCTTTC TGCATGTTTT
 ATAATTTTAA AAAAATTTTT TTCAAATAAT TTTTATTTCA TTTAAATAAT TTTTCAGTGT
 TGACCTTCTA TTGACTGTGA CTTGCAACAT CTAACTGTGG CCATTGGTGT CTGTAGGTCT
 TAGCCCCACG GAGCTGCCAT TTGATTGCCT CGAGAAGACT AGCCGAATGC TCAGCTCCAC
 GTACAACTCT GAGAAGGCTG
 Y
 TGTGAAAACG TGGCGCCACC TCGCCGAGAG CTTCGGCCTG AAGAGGGATG AGATTGGGGG
 CATGACAGAC GGCATGCAAC TCTTTGACCG CATCAGCACG GCAGGCTACA GCATCCCTGA
 GCTACTCACA AAACTGGTGC AGATTGAGCG GCTGGATGCT GTGGAGTCCT TGTGTGCAGA
 CATACTGGAG TGGGCGGGGG TTGTGCCACC TGCCTCCCAG CCACATGCTG CATCCTGAAA
 AGCATGCCTG TGGGCTGTCC TCCCAGGACA AGCCAAGGAG CCAACGAGGG CTCTGGAGCT
 GTGAGTGGTG CCAAAAGACT GCCAAGAATC AAGGCTTTTG TGATATGTCA CCGTATGCCT
 TAGGATGTTC AAGGAGCCAG ACGAAATAAG GCCTGTCTTC CAATTTAACC AAAGATAAAG
 GACTAGAGCC GGGATACTTT CAGATGCTCG CCTGTACCTC ACCAGGCAGA GTAAATATCT
 ACTCACTCAT ACAGCCAGCC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_022171
dbSNP Blast Analysis
UniGene Cluster ID
171971
OMIM
604095.0011

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs3827760 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group		Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1298710038EAS 1008AF 0.873000030.12700000
EUR 1006AF 0.010900000.98909998
AFR 1322AF 0.003000000.99700004
AMR 694AF 0.391900000.60810000
SAS 978AF 0.013300000.98670000
ss161166590ENSEMBL_celera 2IG1.00000000 1.00000000
ss1686464506ExAc_Aggregated_Populations121384AF 0.129036770.87096322
ss23670642AFD_EUR_PANELEuropean 46IG 0.043478260.956521751.000000000.021739130.97826087
AFD_AFR_PANELAfrican American 38IG 0.105263160.894736831.000000000.052631580.94736844
AFD_CHN_PANELAsian 48IG0.958333310.04166667 1.000000000.979166690.02083333
ss238826330pilot_1_CHB+JPT_low_coverage_panel 120AF 0.883333330.11666667
ss342074042ESP_Cohort_Populations 4550GF0.000439560.023296700.976263760.250592000.012087910.98791206
ss44354834HapMap-CEUEuropean 120IG 1.00000000 1.00000000
HapMap-HCBAsian 80IG0.850000020.15000001 1.000000000.925000010.07500000
HapMap-JPTAsian 170IG0.635294140.329411770.035294121.000000000.800000010.20000000
HapMap-YRISub-Saharan African 120IG 1.00000000 1.00000000
HAPMAP-CHBAsian 82IG0.902439000.09756097 1.000000000.951219500.04878049
HAPMAP-CHD 170IG0.847058830.15294118 1.000000000.923529390.07647059
HAPMAP-GIH 176IG 0.034090910.965909061.000000000.017045460.98295456
HAPMAP-MEX 100IG0.180000010.460000010.360000010.751830000.410000000.58999997
ss491789456CSAgilent 1323GF0.003000000.024000000.972999990.001000000.015000000.98500001
ss5014251JBIC-allele 1496AF 0.784700040.21530001
ss80766809KHP1 180AF0.744444430.25555557 0.200325000.872222240.12777779
KHP_Korean 180IG0.744444430.25555557 0.527089000.872222240.12777779

SummaryAverage
Het.+/- std err:		Individual
Count		Founders
Count		Individual
Overlap		Genotype
Conflict		Additional Freq. Data
0.226+/-0.2490000ALFRED: 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
byClusterbyFreqwith2hitwithHapMapFreqWith1000GenomeData
DoubleHit found by:  BCM_SSAHASNP
UNKNOWNUNKNOWNUNKNOWN

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