rs1541331

Homo sapiens
A>G
GTF3C5 : Intron Variant
MIR6877 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0110 (3295/29958,GnomAD)
G=0152 (4426/29118,TOPMED)
G=0138 (692/5008,1000G)
G=0033 (127/3854,ALSPAC)
G=0035 (131/3708,TWINSUK)
chr9:133050630 (GRCh38.p7) (9q34.13)
AD
GWASdb2
1   publication(s)
See rs on genome
128 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.133050630A>G
GRCh37.p13 chr 9NC_000009.11:g.135926017A>G

Gene: GTF3C5, general transcription factor IIIC subunit 5(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GTF3C5 transcript variant 1NM_001122823.1:c.N/AIntron Variant
GTF3C5 transcript variant 3NM_001286709.1:c.N/AIntron Variant
GTF3C5 transcript variant 2NM_012087.3:c.N/AIntron Variant
GTF3C5 transcript variant X1XM_005272234.3:c.N/AIntron Variant
GTF3C5 transcript variant X2XM_011519201.1:c.N/AIntron Variant
GTF3C5 transcript variant X3XM_017015315.1:c.N/AIntron Variant
GTF3C5 transcript variant X4XM_017015316.1:c.N/AIntron Variant

Gene: MIR6877, microRNA 6877(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
MIR6877 transcriptNR_106937.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.655G=0.345
1000GenomesAmericanSub694A=0.970G=0.030
1000GenomesEast AsianSub1008A=0.915G=0.085
1000GenomesEuropeSub1006A=0.956G=0.044
1000GenomesGlobalStudy-wide5008A=0.862G=0.138
1000GenomesSouth AsianSub978A=0.920G=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.967G=0.033
The Genome Aggregation DatabaseAfricanSub8704A=0.693G=0.307
The Genome Aggregation DatabaseAmericanSub838A=0.960G=0.040
The Genome Aggregation DatabaseEast AsianSub1620A=0.931G=0.069
The Genome Aggregation DatabaseEuropeSub18494A=0.974G=0.025
The Genome Aggregation DatabaseGlobalStudy-wide29958A=0.890G=0.110
The Genome Aggregation DatabaseOtherSub302A=0.980G=0.020
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.848G=0.152
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.965G=0.035
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs15413310.000988alcohol dependence20201924

eQTL of rs1541331 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 rs1541331 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 )
chr9135907655135907918E067-18099
chr9135908204135908254E067-17763
chr9135908328135908378E067-17639
chr9135908589135908644E067-17373
chr9135908707135908767E067-17250
chr9135908884135908952E067-17065
chr9135908996135909077E067-16940
chr9135909114135909198E067-16819
chr9135920057135920123E067-5894
chr9135920151135920337E067-5680
chr9135920733135920805E067-5212
chr9135924644135924752E067-1265
chr9135925484135926016E067-1
chr9135926076135926195E06759
chr9135926264135926624E067247
chr9135926626135926937E067609
chr9135927136135927176E0671119
chr9135927196135927289E0671179
chr9135927345135927596E0671328
chr9135878941135879628E068-46389
chr9135879668135879944E068-46073
chr9135879951135880300E068-45717
chr9135880303135880448E068-45569
chr9135904579135904619E068-21398
chr9135904735135904786E068-21231
chr9135907655135907918E068-18099
chr9135923981135924482E068-1535
chr9135924644135924752E068-1265
chr9135925484135926016E068-1
chr9135926076135926195E06859
chr9135926264135926624E068247
chr9135926626135926937E068609
chr9135927136135927176E0681119
chr9135927196135927289E0681179
chr9135927345135927596E0681328
chr9135929598135930791E0683581
chr9135936469135936564E06810452
chr9135936571135937074E06810554
chr9135879668135879944E069-46073
chr9135897579135898207E069-27810
chr9135904240135904412E069-21605
chr9135908204135908254E069-17763
chr9135908328135908378E069-17639
chr9135908589135908644E069-17373
chr9135908707135908767E069-17250
chr9135908884135908952E069-17065
chr9135908996135909077E069-16940
chr9135909114135909198E069-16819
chr9135924644135924752E069-1265
chr9135925484135926016E069-1
chr9135926076135926195E06959
chr9135926264135926624E069247
chr9135926626135926937E069609
chr9135927136135927176E0691119
chr9135927196135927289E0691179
chr9135935691135936188E0699674
chr9135936469135936564E06910452
chr9135936571135937074E06910554
chr9135904579135904619E070-21398
chr9135904735135904786E070-21231
chr9135879668135879944E071-46073
chr9135897579135898207E071-27810
chr9135904240135904412E071-21605
chr9135904579135904619E071-21398
chr9135904735135904786E071-21231
chr9135907655135907918E071-18099
chr9135923981135924482E071-1535
chr9135924644135924752E071-1265
chr9135925484135926016E071-1
chr9135926076135926195E07159
chr9135926264135926624E071247
chr9135926626135926937E071609
chr9135927136135927176E0711119
chr9135927196135927289E0711179
chr9135927345135927596E0711328
chr9135936571135937074E07110554
chr9135879668135879944E072-46073
chr9135879951135880300E072-45717
chr9135880303135880448E072-45569
chr9135897579135898207E072-27810
chr9135907655135907918E072-18099
chr9135923981135924482E072-1535
chr9135924644135924752E072-1265
chr9135925484135926016E072-1
chr9135926076135926195E07259
chr9135926264135926624E072247
chr9135926626135926937E072609
chr9135927136135927176E0721119
chr9135927196135927289E0721179
chr9135927345135927596E0721328
chr9135930845135930918E0724828
chr9135936571135937074E07210554
chr9135904579135904619E073-21398
chr9135904735135904786E073-21231
chr9135907655135907918E073-18099
chr9135919591135919858E073-6159
chr9135920057135920123E073-5894
chr9135920151135920337E073-5680
chr9135923981135924482E073-1535
chr9135924644135924752E073-1265
chr9135925484135926016E073-1
chr9135926076135926195E07359
chr9135926264135926624E073247
chr9135926626135926937E073609
chr9135930845135930918E0734828
chr9135935691135936188E0739674
chr9135936469135936564E07310452
chr9135936571135937074E07310554
chr9135897579135898207E074-27810
chr9135907655135907918E074-18099
chr9135908204135908254E074-17763
chr9135908328135908378E074-17639
chr9135924644135924752E074-1265
chr9135925484135926016E074-1
chr9135926076135926195E07459
chr9135926264135926624E074247
chr9135926626135926937E074609
chr9135927136135927176E0741119
chr9135927196135927289E0741179
chr9135927345135927596E0741328
chr9135935691135936188E0749674
chr9135936469135936564E07410452
chr9135936571135937074E07410554
chr9135907655135907918E081-18099
chr9135908204135908254E081-17763
chr9135908328135908378E081-17639
chr9135908204135908254E082-17763
chr9135908328135908378E082-17639










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr9135905281135906808E067-19209
chr9135906978135907115E067-18902
chr9135905281135906808E068-19209
chr9135906978135907115E068-18902
chr9135905281135906808E069-19209
chr9135906978135907115E069-18902
chr9135905281135906808E070-19209
chr9135906978135907115E070-18902
chr9135905281135906808E071-19209
chr9135906978135907115E071-18902
chr9135905281135906808E072-19209
chr9135906978135907115E072-18902
chr9135905281135906808E073-19209
chr9135906978135907115E073-18902
chr9135905281135906808E074-19209
chr9135906978135907115E074-18902
chr9135905281135906808E081-19209
chr9135906978135907115E081-18902
chr9135905281135906808E082-19209
chr9135906978135907115E082-18902