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Reference SNP (refSNP) Cluster Report: rs41508850                 
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:127/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:C/T (REV)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:NA
MAF/MinorAlleleCount:A=0.3049/1527 (1000 Genomes)
A=0.2340/29386 (TOPMED)
HGVS Names
  • CM000667.2:g.150113108G>A
  • NC_000005.10:g.150113108G>A
  • NC_000005.9:g.149492671G>A
  • NG_012303.1:g.5265C>T
  • NG_023367.1:g.47752C>T
  • NM_005211.3:c.-181+153C>T
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 ss278528544 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs41508850 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
ss66537242SHGC|454fwd/BC/Tgagtcataggctctcctgccgagcccaggctgtgggaccccggcagcaacacagggccag11/01/0611/01/06127Genomicunknown
ss82518851HGSV|Cor19240_SNV_20070510.chr5_149472864rev/TA/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc11/30/0712/03/07130Genomicunknown
ss1134427111000GENOMES|NA19240_2008_12_16_1246987_chr5_149472864rev/TA/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc12/18/0812/18/08130Genomicunknown
ss116856793ILLUMINA-UK|NA18507_000188305_NCBI36.1_chr5_149472864rev/TA/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc01/17/0901/18/09130Genomic99 %
ss156166055GMI|GMI_SNP_273351767rev/TA/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc06/24/0906/25/09131Genomicunknown
ss165967747COMPLETE_GENOMICS|NA19240_36_chr5_149472864rev/TA/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc09/29/0909/30/09132Genomicunknown
ss201017948BUSHMAN|BUSHMAN-chr5-149472863rev/TA/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc02/16/1003/07/10132Genomicunknown
ss2106238911000GENOMES|CEU.trio.3.2010_58806_chr5_149472864rev/TA/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc03/29/1003/29/10132Genomicunknown
ss2220337281000GENOMES|pilot_1_YRI_3843411_chr5_149472864rev/A/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc04/22/1004/22/10132Genomicunknown
ss2331959841000GENOMES|pilot_1_CEU_2800613_chr5_149472864rev/A/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc05/01/1005/01/10132Genomicunknown
ss2403091681000GENOMES|pilot_1_CHB+JPT_2194245_chr5_149472864rev/A/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc05/01/1005/01/10132Genomicunknown
ss278528544GMI|GMI_AK_SNP_2848783rev/A/Gctggccctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctatgactc12/16/1012/16/10137Genomicunknown
ss558791400TISHKOFF|snp_chr5_149492671rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat11/22/1211/23/12138Genomicunknown
ss652695300SSMP|5_149492671rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat12/14/1202/11/15138Genomicunknown
ss982253794EVA-GONL|EVA-GONL_rs41508850rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat04/23/1404/24/14142Genomicunknown
ss1073137414JMKIDD_LAB|HGDP_WGS_chr5_149492671rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat07/10/1407/11/14142Genomicunknown
ss13177295051000GENOMES|PHASE3_V1_29579790rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat08/16/1408/16/14142Genomicunknown
ss1430538329DDI|DDI_rs41508850rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat11/04/1411/05/14144Genomicunknown
ss1581399954EVA_GENOME_DK|EVA_GENOME_DK_snv_rs41508850rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat02/19/1502/20/15144Genomicunknown
ss1591786570EVA_DECODE|EVA_DECODE_5_149472864_1117275_rs41508850rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat03/02/1503/03/15144Genomicunknown
ss1614287889EVA_UK10K_ALSPAC|EVA_UK10K_ALSPAC_5_149492671_16373375rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat03/04/1503/04/15144Genomicunknown
ss1657281922EVA_UK10K_TWINSUK|EVA_UK10K_TWINSUK_5_149492671_16373375rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat03/04/1503/04/15144Genomicunknown
ss1804136307HAMMER_LAB|Hsieh_3145220rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat07/15/1507/15/15146Genomicunknown
ss1925507728WEILL_CORNELL_DGM|SNV:chr5:149492671rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat10/16/1510/17/15147Genomicunknown
ss1958834029ILLUMINA|rs41508850-138_B_F_2286767346rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat11/13/1511/13/15147Genomicunknown
ss2023361688JJLAB|SNP3864243rev/TA/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat08/29/1608/30/16149Genomicunknown
ss2151520224USC_VALOUEV|NC_000005.9:g.149492671G>Arev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat11/17/1611/17/16150Genomicunknown
ss2279232014HUMAN_LONGEVITY|HLI-5-150113108-G-Arev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat11/18/1611/18/16150Genomicunknown
ss2447550849TOPMED|5_149492671_G/Arev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat11/20/1611/20/16150Genomicunknown
ss2626169434SYSTEMSBIOZJU|SYSTEMSBIOZJU_SNV2473351rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat01/06/1701/06/17151Genomicunknown
ss2635150311ILLUMINA|Cancer_BeadChip_11459870_A_rs41508850-128_T_R_1673455767rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat02/02/1702/02/17151Genomicunknown
ss2707089950GRF|rs41508850rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat02/13/1702/13/17151Genomicunknown
ss2832248550GNOMAD|rs41508850rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat05/18/1705/18/17151Genomicunknown
ss2997996981SWEGEN|NC_000005.9:g.149492671G>Arev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat05/30/1705/30/17151Genomicunknown
ss3022542254ILLUMINA|MEGA_Consortium_v2_15070954_A2_rs41508850-138_B_F_2286767346rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat06/28/1706/28/17151Genomicunknown
ss3025462671BIOINF_KMB_FNS_UNIBA|5.150113108G>Arev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat07/05/1707/05/17151Genomicunknown
ss3346682729CSHL|rs41508850rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat10/02/1710/02/17151Genomicunknown
ss3482057673TOPMED|TOPMed_freeze_5?chr5:150,113,108rev/A/Gcctgtgttgctgccggggtcccacagcctgggctcggcaggagagcctat10/04/1710/04/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs41508850|allelePos=501|totalLen=1001|taxid=9606|snpclass=1|alleles='C/T'|mol=Genomic|build=151
 ACAGAGCCTG GCCTTGAGTC GGGCAGGAGG GTGTGGGGCT GCAGGGCTGC TCCAAGGCTC
 TGGTGCTGAG GCGTCTCACT GCCTCCACCA TGTGCTTTGG CTTTGGCTAT CAGCTGGGAC
 ACCCTCCCCT CCACTCCGCC CACAGGCCCG GATTGAGGCC GGCGTGCTCT GTGACAGGCA
 GCTGCTAGAG CCCAGATTCC AGGTCCAGGT GAGTCATGAT CAGGCCCCAG GTAGGAGAAG
 GGCAGACAGA GTGTCCAAAA GCGTGAGAGC ACGAAGTGAG GAGAAGGTGG AGAAGAGAGA
 AGAGGAAGAG GAAGAGGAAG AGAGGAAGCG GAGGGAACTG CGGCCAGGGT AAGGACAGGG
 GAGGGAATAG GGTGGCGACC AGGCTGTGGC TTTGAGGGCA GAGAGGTGTA GACCTGGCAG
 GACCCAGACC CCTCACGGCT GCAGCATCTC AGGGGTTGTG GGGCCGGCAT GAGTCATAGG
 CTCTCCTGCC GAGCCCAGGC
 Y
 TGTGGGACCC CGGCAGCAAC ACAGGGCCAG GGGCAATAGG GTTGCTGGGG GCAGGGGACA
 GAGTGCTAGG GCCCTCCCAC CTGGGCCCAG AGTCCTGTAC TTGGCTCACT TGAGGTGGAC
 CAGATGTCAG CCTCAGATCC ATCACTGTGT GTCCTTAGCC CCTCCCTTGC TCTCTCTGAG
 CTGGGGAAAC GGCATCTTCA TTTGAGTGGG TGCGGGAAGG ACCTCATTTT GGAACCACAG
 GCCTCCCTGG ACTGCCTCCA GGAGTCTGGG GCTGTGGCTT CAAGTGGGGA AAAGAATGGA
 GCCATGGGAC AGCTCTGACT CACAGGCCCA GCCGCCAACT CAGGGGCAGC TGAGCCACAC
 CAGGGAAAAT ACCCGACGGC TATAAGGCCT GGCCATACAA AGCCCACCAT CCCAGGGATC
 CTGGCTTCAG AAAACACCCA GAGCCTGTGA CTTCTCTTCT AGCTGTGGCA GGAGTTGAAT
 GAGGTGATAC CCGGATCTGC

  NCBI Resource Links back to top
Submitter-Referenced
GenBank
NM_005211.2
dbSNP Blast Analysis

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] Note: rs41508850 allele is reverse to the genome back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/T
T/T
HWPC
T
ss116856793YRI 2IG1.00000000 0.500000000.50000000
ss1317729505EAS 1008AF 0.565499960.43450001
EUR 1006AF 0.867800000.13219999
AFR 1322AF 0.500000000.50000000
AMR 694AF 0.827099980.17290001
SAS 978AF 0.821100060.17890000
ss165967747YRISub-Saharan African 2IG 1.00000000 1.00000000
ss222033728pilot_1_YRI_low_coverage_panel 118AF 0.483050850.51694918
ss233195984pilot_1_CEU_low_coverage_panel 120AF 0.941666660.05833333
ss240309168pilot_1_CHB+JPT_low_coverage_panel 120AF 0.483333320.51666665
ss66537242R24 26AF 0.959999980.04000000

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.424+/-0.1800000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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