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Reference SNP (refSNP) Cluster Report: rs7988257                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:116/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqwith2hitWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/T (FWD)
Allele Origin:
Ancestral Allele:A
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.3838/1922 (1000 Genomes)
A=0.2898/36395 (TOPMED)
HGVS Names
  • CM000675.2:g.92813286C>A
  • CM000675.2:g.92813286C>T
  • NC_000013.10:g.93465539C>A
  • NC_000013.11:g.92813286C>A
  • NC_000013.11:g.92813286C>T
  • NG_009370.1:g.1419605C>A
  • NG_009370.1:g.1419605C>T
  • NM_004466.5:c.1562-52996C>A
  • NM_004466.5:c.1562-52996C>T
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 ss281835102 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs7988257 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
ss12241742WI_SSAHASNP|chr13.NT_009952.13_6555214byFreqfwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt07/04/0305/17/04116Genomicunknown
ss13273396SC_SNP|NT_009952.13_6555214fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt10/22/0302/27/04119Genomicunknown
ss23810577PERLEGEN|afd2158412byFreqfwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt08/10/0409/13/04123Genomicunknown
ss65813692ILLUMINA|Human1-rs7988257fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt10/10/0610/10/06127Genomicunknown
ss66660735ILLUMINA|HumanHap300v1.1_rs7988257fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt11/09/0611/09/06127Genomicunknown
ss67856800ILLUMINA|HumanHap550v1.1_rs7988257fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt11/14/0611/14/06127Genomicunknown
ss68007361ILLUMINA|HumanHap650Yv1.0_rs7988257fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt11/14/0611/15/06127Genomicunknown
ss70962967ILLUMINA|HumanHap550v3.0__rs7988257fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt04/20/0703/31/08130Genomicunknown
ss71571945ILLUMINA|HumanHap650Yv3.0_rs7988257fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt04/23/0704/23/07127Genomicunknown
ss75500878ILLUMINA|ILMN_Human_1M_rs7988257fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt08/28/0708/29/07129Genomicunknown
ss76718852AFFY|AFFY_6_1M_SNP_A-8580128rev/BG/Tttattttgattcctcccagtggccttacttaa08/28/0708/30/07129Genomicunknown
ss79277208ILLUMINA|HumanHap300v2.0_rs7988257fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt04/18/0711/18/07130Genomicunknown
ss81483054HGSV|Cor18555_SNV_20070510.chr13_92263540fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt11/27/0711/30/07130Genomicunknown
ss84764131KRIBB_YJKIM|KHS802852fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt12/04/0712/07/07130Genomicunknown
ss1079963241000GENOMES|CEU.trio.12.15.2008_2963258_chr13_92263540fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt12/15/0812/15/08130Genomicunknown
ss1151148931000GENOMES|NA19240_2008_12_16_2657487_chr13_92263540fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt12/19/0812/19/08130Genomicunknown
ss118932021ILLUMINA-UK|NA18507_000101731_NCBI36.1_chr13_92263540byFreqfwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt01/21/0909/05/14130Genomic99 %
ss122877323ILLUMINA|HumanCNV370v1_C_rs7988257fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt04/14/0904/15/09131Genomicunknown
ss154461132ILLUMINA|Human610_Quadv1_B_rs7988257-127_T_F_1501871750fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt06/18/0906/20/09131Genomicunknown
ss159635730ILLUMINA|Human660W-Quad_v1_A_rs7988257-128_T_F_1501871750fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt07/06/0907/07/09131Genomicunknown
ss160936855ILLUMINA|HumanOmni1-Quad_v1-0_B_rs7988257-128_T_F_1501871750fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt08/04/0910/05/09131Genomicunknown
ss170453420COMPLETE_GENOMICS|NA19240_36_chr13_92263540fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt10/01/0910/01/09132Genomicunknown
ss172379535ILLUMINA|HumanCNV370-Quadv3_C_rs7988257-127_T_F_1501871750fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt10/01/0910/04/09132Genomicunknown
ss174656147ILLUMINA|Human1M-Duov3_B_rs7988257-127_T_F_1501871750fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt10/01/0910/04/09132Genomicunknown
ss199561961BUSHMAN|BUSHMAN-chr13-92263539fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt02/16/1003/06/10132Genomicunknown
ss2263477951000GENOMES|pilot_1_YRI_8157478_chr13_92263540fwd/A/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt04/22/1004/22/10132Genomicunknown
ss2363792861000GENOMES|pilot_1_CEU_5983915_chr13_92263540fwd/A/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt05/01/1005/01/10132Genomicunknown
ss2428458821000GENOMES|pilot_1_CHB+JPT_4730959_chr13_92263540fwd/A/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt05/01/1005/01/10132Genomicunknown
ss255241089BL|SNP87499_13_92263540fwd/TA/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt08/19/1008/20/10134Genomicunknown
ss281835102GMI|GMI_AK_SNP_6155491fwd/A/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt12/16/1012/16/10137Genomicunknown
ss291507759PJP|SNP_1014117_chr13_92263540fwd/A/Caactgctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaatctttt01/21/1101/21/11134Genomicunknown
ss481742801ILLUMINA|HumanOmni2.5-4v1_B_rs7988257-128_T_F_1767544077fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat01/30/1210/28/16137Genomicunknown
ss481774592ILLUMINA|HumanOmniExpress-12v1_C_rs7988257-131_T_F_1859578296fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat01/30/1210/27/16137Genomicunknown
ss482739181ILLUMINA|HumanOmni1-Quad_v1-0_C_rs7988257-131_T_F_1859578296fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat01/30/1208/28/15146Genomicunknown
ss485666150ILLUMINA|HumanOmni2.5-4v1_D_rs7988257-131_T_F_1859578296fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat01/30/1210/27/16137Genomicunknown
ss537540317ILLUMINA|HumanOmni5-4v1_B_rs7988257-131_T_F_1866843741fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat06/22/1208/29/15146Genomicunknown
ss563842194TISHKOFF|snp_chr13_93465539fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat11/22/1211/23/12138Genomicunknown
ss659482325SSMP|13_93465539fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat12/14/1202/13/15138Genomicunknown
ss778993459ILLUMINA|HumanOmni25Exome-8v1_A_rs7988257-131_T_F_1866843741fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat05/30/1307/10/15146Genomicunknown
ss783278649ILLUMINA|HumanOmni2.5-4v1_H_rs7988257-131_T_F_1859578296fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat05/30/1307/29/15146Genomicunknown
ss784231676ILLUMINA|HumanOmniExpressExome-8v1_A_rs7988257-131_T_F_1866843741fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat05/31/1306/18/15146Genomicunknown
ss825607726ILLUMINA|HumanCNV370v1_C_rs7988257-123_T_F_IFB1135601494:0fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat06/24/1311/21/14144Genomicunknown
ss832539760ILLUMINA|HumanOmniExpress-12v1_H_rs7988257-131_T_F_1859578296fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat09/17/1306/18/15146Genomicunknown
ss834455738ILLUMINA|HumanOmni2.5-8v1_A_rs7988257-131_T_F_1866843741fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat09/18/1307/29/15146Genomicunknown
ss990718684EVA-GONL|EVA-GONL_rs7988257fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat04/23/1404/25/14142Genomicunknown
ss1079334471JMKIDD_LAB|HGDP_WGS_chr13_93465539fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat07/10/1407/12/14142Genomicunknown
ss13494086771000GENOMES|PHASE3_V1_62566106fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat08/16/1408/16/14142Genomicunknown
ss1427287331DDI|DDI_rs7988257fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat11/04/1411/04/14144Genomicunknown
ss1576988508EVA_GENOME_DK|EVA_GENOME_DK_snv_rs7988257fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat02/19/1502/19/15144Genomicunknown
ss1630904845EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_13_93465539_34628726fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat03/04/1503/04/15144Genomicunknown
ss1673898878EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_13_93465539_34628726fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat03/04/1503/04/15144Genomicunknown
ss1694707979EVA_DECODE|EVA_DECODE_13_92263540_591629_rs7988257fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat03/02/1503/04/15144Genomicunknown
ss1713412659EVA_SVP|EVA_SVP_1107026fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat03/12/1503/12/15144Genomicunknown
ss1752118061ILLUMINA|OmniExpressExome-8v1-1_B_rs7988257-131_T_F_1866843741fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat05/27/1506/09/15146Genomicunknown
ss1807738059HAMMER_LAB|Hsieh_6761195fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat07/15/1507/16/15146Genomicunknown
ss1934078750WEILL_CORNELL_DGM|SNV:chr13:93465539fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat10/16/1510/17/15147Genomicunknown
ss1959520199ILLUMINA|rs7988257-138_T_F_2276729532fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat11/13/1511/13/15147Genomicunknown
ss2027812195JJLAB|SNP8314750fwd/TA/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat08/29/1608/31/16149Genomicunknown
ss2156178762USC_VALOUEV|NC_000013.10:g.93465539C>Afwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat11/17/1611/17/16150Genomicunknown
ss2198826279HUMAN_LONGEVITY|HLI-13-92813286-C-Afwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat11/18/1611/18/16150Genomicunknown
ss2363012062TOPMED|13_93465539_C/Tfwd/C/Tctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat11/19/1611/19/16150Genomicunknown
ss2628393057SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV5304008fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat01/06/1701/06/17151Genomicunknown
ss2633097780ILLUMINA|SoL_HCHS_Custom_15041502_B3_RefStrand_rs7988257-131_T_F_18668437fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat02/02/1702/02/17151Genomicunknown
ss2700571605GRF|rs7988257fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat02/13/1702/13/17151Genomicunknown
ss2923056836GNOMAD|rs7988257fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat05/23/1705/23/17151Genomicunknown
ss3011511569SWEGEN|NC_000013.10:g.93465539C>Afwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat05/30/1705/30/17151Genomicunknown
ss3021529970ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs7988257-138_T_F_2276729532fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat06/28/1706/28/17151Genomicunknown
ss3027726764BIOINF_KMB_FNS_UNIBA|13.92813286C>Afwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat07/05/1707/05/17151Genomicunknown
ss3200589731TOPMED|TOPMed_freeze_5?chr13:92,813,286-01fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat09/30/1709/30/17151Genomicunknown
ss3200589732TOPMED|TOPMed_freeze_5?chr13:92,813,286-02fwd/C/Tctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat09/30/1709/30/17151Genomicunknown
ss3350603047CSHL|rs7988257fwd/A/Cctggtcattttaagtaaggccactgggaggaatcaaaataattttgtaat10/02/1710/02/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs7988257|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='A/C/T'|mol=Genomic|build=151
 ACTCCATGAT GTCTCTATAC ACTTGTAATG AATGCCATGA GAAGAAAATT AAGATTTTTA
 TTTGTATGCA AGACTTGTTT TATACACTCA AATTTTGAAT AGTTTCCAAT TTTTCCAAGA
 TTCATAATCT CAGAACTTCT CTAAATAATT TATTTTAGAT TTTCCTCATC AGTCTTATCT
 TCTAAAATTT AATTCACCAA TTCTTATAAA ATGAAGTGTA TTTTTTATCA TACAAGAAAA
 ATGATAAAGT TAAAAGACTC CTATTTTAAA TACCGGCCTT TCGAAGCTTA TTTACATAAT
 GGGAAAATAT TGTTATATTT TAAATAATCC TTACCATGCA GGACTGGTTT TATTGCTCTA
 ACTTGGAGTT CTGTAATTCT GGCTGGTCAG AACCCCAAGG CATCCTAACA ATGTCAGAAA
 CGAGTCTCCT GATCCATTTT TGTTGAAATA AGATTGGAAT TTCCTATGAA AACTGCTGGT
 CATTTTAAGT AAGGCCACTG
 H
 GGAGGAATCA AAATAATTTT GTAATCTTTT TTTTAGTTCT GATTATGGTT AGACACAATT
 CATAATAATG AACACGTTTT AAATAAAAAC GTAGTTCTTA CTTGAAAGTT CTAATATTCT
 TAAACCTCAT TGCTTTATAA AATTTGTCCA GGTGATCATC TCTTATTCAG CATTCCCACA
 GCTTCTACTC CTGCCCTTTT CCCTCCATAG TTCCAAACTA ATTTTATGCA AATACATGTG
 TTAGATTTAT TTTTAGGAAT TGTTCAACAT GAAAGCAAAT AATAAATTCA GTTAACAAAA
 TGGTAGGTAT GTGTTTGGGA ATATGAAAGA TGCAAAGATG GCGCAATACT TTTAGTCAAA
 ACTTTTTTCA ATGTTATATA AACAGTAGTA TTCTTTACCA AAAATGTACA ATTCTTCTAC
 ACTGAAAATT GCAAAGCATT GCTGAGAGTA AACAAAGAAG ACCTAAATAA GTGGCGAGAT
 GTAACATGCT CATGTTCTAA

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NT_009952
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
A/C
C
C/C
HWPA
C
ss118932021HapMap-CEUEuropean 222IG 0.009009010.25225225 0.738738720.438578000.135135130.86486489
HapMap-HCBAsian 86IG 0.093023260.48837209 0.418604640.583882000.337209310.66279072
HapMap-JPTAsian 168IG 0.190476190.52380955 0.285714300.654721000.452380960.54761904
HapMap-YRISub-Saharan African 226IG 0.451327440.46902654 0.079646020.371093000.685840730.31415930
HAPMAP-CHBAsian 80IG 0.200000000.32499999 0.474999990.099721000.362500010.63749999
HAPMAP-CHD 170IG 0.094117650.43529412 0.470588241.000000000.311764720.68823528
HAPMAP-GIH 176IG 0.136363640.47727272 0.386363631.000000000.375000000.62500000
HAPMAP-LWK 180IG 0.355555560.52222222 0.122222220.342782000.616666670.38333333
HAPMAP-MEX 100IG 0.060000000.36000001 0.579999981.000000000.239999990.75999999
HAPMAP-MKK 282IG 0.276595740.50354612 0.219858151.000000000.528368770.47163120
HAPMAP-TSI 174IG 0.26436782 0.735632180.527089000.132183910.86781609
ENSEMBL_Watson 2IG 1.00000000 1.00000000
YRI 2IG 1.00000000 0.500000000.50000000
ENSEMBL_Venter 2IG 1.00000000 1.00000000
ss12241742CHMJAsian 74IG0.37837839 0.62162161 0.378378390.62162161
ss1349408677EAS 1008AF 0.368099990.63190001
EUR 1006AF 0.132199990.86780000
AFR 1322AF 0.667900030.33210000
AMR 694AF 0.204600010.79540002
SAS 978AF 0.401799980.59820002
ss170453420YRISub-Saharan African 2IG 1.00000000 1.00000000
ss199561961BUSHMAN_POP2 2IG 1.00000000 0.500000000.50000000
ss226347795pilot_1_YRI_low_coverage_panel 118AF 0.703389820.29661018
ss236379286pilot_1_CEU_low_coverage_panel 120AF 0.158333330.84166664
ss23810577AFD_EUR_PANELEuropean 48IG 0.16666667 0.833333311.000000000.083333340.91666669
AFD_AFR_PANELAfrican American 46IG 0.434782590.39130434 0.173913050.479500000.630434810.36956522
AFD_CHN_PANELAsian 46IG 0.086956520.52173913 0.391304340.479500000.347826090.65217394
ss242845882pilot_1_CHB+JPT_low_coverage_panel 120AF 0.316666660.68333334

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
Additional Freq. Data
0.473+/-0.1130000ALFRED: 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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