rs6081377

Homo sapiens
T>C
LINC00652 : 2KB Upstream Variant
LOC100270804 : 500B Downstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0356 (10670/29902,GnomAD)
C=0361 (10514/29118,TOPMED)
C=0288 (1440/5008,1000G)
C=0388 (1495/3854,ALSPAC)
C=0380 (1410/3708,TWINSUK)
chr20:18796142 (GRCh38.p7) (20p11.23)
AD
GWASdb2
1   publication(s)
See rs on genome
71 Enhancers around
21 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.18796142T>C
GRCh37.p13 chr 20NC_000020.10:g.18776786T>C

Gene: LINC00652, long intergenic non-protein coding RNA 652(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LINC00652 transcript variant 1NR_026883.1:n.N/AUpstream Transcript Variant
LINC00652 transcript variant 2NR_026884.1:n.N/AN/A

Gene: LOC100270804, uncharacterized LOC100270804(plus strand): 500B Downstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC100270804 transcriptNR_026885.1:n.N/ADownstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.666C=0.334
1000GenomesAmericanSub694T=0.690C=0.310
1000GenomesEast AsianSub1008T=0.893C=0.107
1000GenomesEuropeSub1006T=0.635C=0.365
1000GenomesGlobalStudy-wide5008T=0.712C=0.288
1000GenomesSouth AsianSub978T=0.690C=0.310
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.612C=0.388
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.638C=0.361
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.620C=0.380
PMID Title Author Journal
23953852Genome-wide association studies of maximum number of drinks.Pan YJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs60813779.4E-07alcohol consumption23953852

eQTL of rs6081377 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs6081377 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr201873006618730242E067-46544
chr201873035618730483E067-46303
chr201873052718730577E067-46209
chr201873067218731219E067-45567
chr201873135218731419E067-45367
chr201873150318731793E067-44993
chr201873067218731219E068-45567
chr201873135218731419E068-45367
chr201873150318731793E068-44993
chr201877564318775827E068-959
chr201873035618730483E069-46303
chr201873052718730577E069-46209
chr201873067218731219E069-45567
chr201873135218731419E069-45367
chr201873150318731793E069-44993
chr201872937818729456E070-47330
chr201872969918729881E070-46905
chr201873006618730242E070-46544
chr201873135218731419E070-45367
chr201873150318731793E070-44993
chr201877564318775827E070-959
chr201882035118820497E07043565
chr201882057518820992E07043789
chr201882103718821130E07044251
chr201872969918729881E071-46905
chr201873006618730242E071-46544
chr201873035618730483E071-46303
chr201873052718730577E071-46209
chr201873067218731219E071-45567
chr201873135218731419E071-45367
chr201873150318731793E071-44993
chr201873181618731860E071-44926
chr201877564318775827E071-959
chr201877584718776003E071-783
chr201873006618730242E072-46544
chr201873035618730483E072-46303
chr201873052718730577E072-46209
chr201873067218731219E072-45567
chr201873135218731419E072-45367
chr201873150318731793E072-44993
chr201873135218731419E073-45367
chr201872969918729881E074-46905
chr201873006618730242E074-46544
chr201873035618730483E074-46303
chr201873052718730577E074-46209
chr201873067218731219E074-45567
chr201873135218731419E074-45367
chr201873150318731793E074-44993
chr201872937818729456E081-47330
chr201872969918729881E081-46905
chr201873006618730242E081-46544
chr201873035618730483E081-46303
chr201873052718730577E081-46209
chr201873067218731219E081-45567
chr201873135218731419E081-45367
chr201873150318731793E081-44993
chr201872937818729456E082-47330
chr201872969918729881E082-46905
chr201873006618730242E082-46544
chr201873035618730483E082-46303
chr201873052718730577E082-46209
chr201873067218731219E082-45567
chr201873135218731419E082-45367
chr201873150318731793E082-44993
chr201873181618731860E082-44926
chr201873208118732131E082-44655
chr201877564318775827E082-959
chr201877584718776003E082-783
chr201877605918776167E082-619
chr201877620818776294E082-492
chr201877639118776475E082-311










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr201877420018774250E067-2536
chr201877430018775630E067-1156
chr201877408218774171E068-2615
chr201877420018774250E068-2536
chr201877430018775630E068-1156
chr201877420018774250E069-2536
chr201877430018775630E069-1156
chr201877420018774250E070-2536
chr201877430018775630E070-1156
chr201877420018774250E071-2536
chr201877430018775630E071-1156
chr201877420018774250E072-2536
chr201877430018775630E072-1156
chr201877420018774250E073-2536
chr201877430018775630E073-1156
chr201877420018774250E074-2536
chr201877430018775630E074-1156
chr201877420018774250E081-2536
chr201877430018775630E081-1156
chr201877420018774250E082-2536
chr201877430018775630E082-1156