rs854104

Homo sapiens
A>C / A>G
LOC105375409 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0101 (3021/29804,GnomAD)
A==0106 (3101/29118,TOPMED)
A==0156 (780/5008,1000G)
A==0094 (361/3854,ALSPAC)
A==0097 (359/3708,TWINSUK)
chr7:95696422 (GRCh38.p7) (7q21.3)
AD
GWASdb2
1   publication(s)
See rs on genome
84 Enhancers around
92 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.95696422A>C
GRCh38.p7 chr 7NC_000007.14:g.95696422A>G
GRCh37.p13 chr 7NC_000007.13:g.95325734A>C
GRCh37.p13 chr 7NC_000007.13:g.95325734A>G

Gene: LOC105375409, uncharacterized LOC105375409(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105375409 transcript variant X2XR_927774.2:n.N/AIntron Variant
LOC105375409 transcript variant X1XR_927772.2:n.N/AGenic Downstream Transcript Variant
LOC105375409 transcript variant X2XR_927773.2:n.N/AGenic Downstream Transcript Variant
LOC105375409 transcript variant X4XR_927775.2:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.076G=0.924
1000GenomesAmericanSub694A=0.210G=0.790
1000GenomesEast AsianSub1008A=0.258G=0.742
1000GenomesEuropeSub1006A=0.116G=0.884
1000GenomesGlobalStudy-wide5008A=0.156G=0.844
1000GenomesSouth AsianSub978A=0.160G=0.840
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.094G=0.906
The Genome Aggregation DatabaseAfricanSub8712A=0.068C=0.000
The Genome Aggregation DatabaseAmericanSub834A=0.190C=0.00,
The Genome Aggregation DatabaseEast AsianSub1558A=0.233C=0.000
The Genome Aggregation DatabaseEuropeSub18398A=0.102C=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29804A=0.101C=0.000
The Genome Aggregation DatabaseOtherSub302A=0.080C=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.106G=0.893
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.097G=0.903
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs8541046.25E-05alcohol dependence21703634

eQTL of rs854104 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 rs854104 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 )
chr75614668356146748E067-2351
chr75614694056147914E067-1185
chr75615088656151247E0671787
chr75615129556151454E0672196
chr75611768656117772E068-31327
chr75614177056142457E068-6642
chr75614246056142521E068-6578
chr75614620256146475E068-2624
chr75614649656146546E068-2553
chr75614668356146748E068-2351
chr75615088656151247E0681787
chr75615129556151454E0682196
chr75615149756151555E0682398
chr75615931256159723E06810213
chr75617262556172679E06823526
chr75612086556120915E069-28184
chr75612106156121170E069-27929
chr75614177056142457E069-6642
chr75614668356146748E069-2351
chr75614694056147914E069-1185
chr75615149756151555E0692398
chr75616027856161160E06911179
chr75612086556120915E070-28184
chr75612106156121170E070-27929
chr75614694056147914E070-1185
chr75615088656151247E0701787
chr75615129556151454E0702196
chr75616027856161160E07011179
chr75614620256146475E071-2624
chr75614649656146546E071-2553
chr75614668356146748E071-2351
chr75614694056147914E071-1185
chr75614959956149820E071500
chr75614992656149976E071827
chr75615088656151247E0711787
chr75615129556151454E0712196
chr75615149756151555E0712398
chr75615830056158396E0719201
chr75615931256159723E07110213
chr75617148856171551E07122389
chr75617262556172679E07123526
chr75612086556120915E072-28184
chr75612106156121170E072-27929
chr75613341556133559E072-15540
chr75614620256146475E072-2624
chr75614649656146546E072-2553
chr75614668356146748E072-2351
chr75614694056147914E072-1185
chr75615088656151247E0721787
chr75615129556151454E0722196
chr75615149756151555E0722398
chr75616027856161160E07211179
chr75611768656117772E073-31327
chr75612086556120915E073-28184
chr75612106156121170E073-27929
chr75614566056145710E073-3389
chr75614581156145868E073-3231
chr75614591056146038E073-3061
chr75614608956146162E073-2937
chr75614620256146475E073-2624
chr75614649656146546E073-2553
chr75614668356146748E073-2351
chr75614694056147914E073-1185
chr75615088656151247E0731787
chr75615129556151454E0732196
chr75615819356158233E0739094
chr75615830056158396E0739201
chr75616027856161160E07311179
chr75612086556120915E074-28184
chr75612106156121170E074-27929
chr75614177056142457E074-6642
chr75614694056147914E074-1185
chr75615088656151247E0741787
chr75615129556151454E0742196
chr75615931256159723E07410213
chr75611768656117772E081-31327
chr75612086556120915E081-28184
chr75612106156121170E081-27929
chr75614694056147914E081-1185
chr75617262556172679E08123526
chr75611712156117191E082-31908
chr75611768656117772E082-31327
chr75612224656122296E082-26803
chr75614694056147914E082-1185










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr75610131056102370E067-46729
chr75611863156120353E067-28746
chr75613123156132326E067-16773
chr75613234956132463E067-16636
chr75613254956132603E067-16496
chr75613270956133194E067-15905
chr75617307356174530E06723974
chr75618399356184259E06734894
chr75618428856184397E06735189
chr75610131056102370E068-46729
chr75611863156120353E068-28746
chr75613123156132326E068-16773
chr75613234956132463E068-16636
chr75613254956132603E068-16496
chr75613270956133194E068-15905
chr75617307356174530E06823974
chr75617462856175211E06825529
chr75618358956183963E06834490
chr75618399356184259E06834894
chr75618428856184397E06835189
chr75610131056102370E069-46729
chr75611863156120353E069-28746
chr75613123156132326E069-16773
chr75613234956132463E069-16636
chr75613254956132603E069-16496
chr75613270956133194E069-15905
chr75617307356174530E06923974
chr75618399356184259E06934894
chr75618428856184397E06935189
chr75610131056102370E070-46729
chr75611863156120353E070-28746
chr75613123156132326E070-16773
chr75613234956132463E070-16636
chr75613254956132603E070-16496
chr75613270956133194E070-15905
chr75617307356174530E07023974
chr75618358956183963E07034490
chr75618399356184259E07034894
chr75610131056102370E071-46729
chr75611863156120353E071-28746
chr75613123156132326E071-16773
chr75613234956132463E071-16636
chr75613254956132603E071-16496
chr75613270956133194E071-15905
chr75617307356174530E07123974
chr75618358956183963E07134490
chr75618399356184259E07134894
chr75618428856184397E07135189
chr75610131056102370E072-46729
chr75611863156120353E072-28746
chr75613123156132326E072-16773
chr75613234956132463E072-16636
chr75613254956132603E072-16496
chr75613270956133194E072-15905
chr75617307356174530E07223974
chr75617462856175211E07225529
chr75618358956183963E07234490
chr75618399356184259E07234894
chr75618428856184397E07235189
chr75610131056102370E073-46729
chr75611863156120353E073-28746
chr75613123156132326E073-16773
chr75613234956132463E073-16636
chr75613254956132603E073-16496
chr75613270956133194E073-15905
chr75617307356174530E07323974
chr75618358956183963E07334490
chr75618399356184259E07334894
chr75618428856184397E07335189
chr75610131056102370E074-46729
chr75611863156120353E074-28746
chr75613123156132326E074-16773
chr75613234956132463E074-16636
chr75613254956132603E074-16496
chr75613270956133194E074-15905
chr75617307356174530E07423974
chr75610131056102370E081-46729
chr75611863156120353E081-28746
chr75613123156132326E081-16773
chr75613234956132463E081-16636
chr75613254956132603E081-16496
chr75613270956133194E081-15905
chr75617307356174530E08123974
chr75610131056102370E082-46729
chr75611863156120353E082-28746
chr75613123156132326E082-16773
chr75613234956132463E082-16636
chr75613254956132603E082-16496
chr75613270956133194E082-15905
chr75617307356174530E08223974
chr75618358956183963E08234490
chr75618399356184259E08234894