rs9680399

Homo sapiens
G>A
LINC00319 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0094 (2813/29908,GnomAD)
A=0106 (3092/29116,TOPMED)
A=0115 (578/5008,1000G)
A=0139 (537/3854,ALSPAC)
A=0137 (509/3708,TWINSUK)
chr21:43451183 (GRCh38.p7) (21q22.3)
AD
GWASdb2
1   publication(s)
See rs on genome
201 Enhancers around
16 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 21NC_000021.9:g.43451183G>A
GRCh37.p13 chr 21NC_000021.8:g.44871063G>A

Gene: LINC00319, long intergenic non-protein coding RNA 319(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC00319 transcriptNR_026960.1:n.909G>AG>ANon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.921A=0.079
1000GenomesAmericanSub694G=0.930A=0.070
1000GenomesEast AsianSub1008G=0.904A=0.096
1000GenomesEuropeSub1006G=0.860A=0.140
1000GenomesGlobalStudy-wide5008G=0.885A=0.115
1000GenomesSouth AsianSub978G=0.810A=0.190
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.861A=0.139
The Genome Aggregation DatabaseAfricanSub8700G=0.922A=0.078
The Genome Aggregation DatabaseAmericanSub836G=0.920A=0.080
The Genome Aggregation DatabaseEast AsianSub1620G=0.910A=0.090
The Genome Aggregation DatabaseEuropeSub18450G=0.898A=0.101
The Genome Aggregation DatabaseGlobalStudy-wide29908G=0.905A=0.094
The Genome Aggregation DatabaseOtherSub302G=0.810A=0.190
Trans-Omics for Precision MedicineGlobalStudy-wide29116G=0.893A=0.106
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.863A=0.137
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
rs96803990.000664alcohol dependence20201924

eQTL of rs9680399 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 rs9680399 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 )
chr214488387244884287E06712809
chr214486255444863210E068-7853
chr214486334544863530E068-7533
chr214487613044876420E0685067
chr214487728044877330E0686217
chr214487735344877434E0686290
chr214487745044877520E0686387
chr214489745244898430E06826389
chr214489858444898670E06827521
chr214487552644875995E0694463
chr214487599744876095E0694934
chr214487613044876420E0695067
chr214487735344877434E0696290
chr214487745044877520E0696387
chr214482296444823071E070-47992
chr214482314544824342E070-46721
chr214482885344828893E070-42170
chr214482890644828999E070-42064
chr214482902144832796E070-38267
chr214485169444851869E070-19194
chr214485192544852005E070-19058
chr214486953044869708E070-1355
chr214486974544869819E070-1244
chr214486987344869996E070-1067
chr214487003344870388E070-675
chr214487056244870647E070-416
chr214487075044870881E070-182
chr214488280344883350E07011740
chr214488335544883457E07012292
chr214488351144883785E07012448
chr214488387244884287E07012809
chr214490579344905843E07034730
chr214490596144906261E07034898
chr214490626344906472E07035200
chr214487003344870388E071-675
chr214487056244870647E071-416
chr214487075044870881E071-182
chr214487716244877224E0716099
chr214487728044877330E0716217
chr214487735344877434E0716290
chr214487745044877520E0716387
chr214488280344883350E07111740
chr214488351144883785E07112448
chr214488387244884287E07112809
chr214482160244821681E072-49382
chr214482170544822092E072-48971
chr214487552644875995E0724463
chr214487599744876095E0724934
chr214487613044876420E0725067
chr214487642244877004E0725359
chr214487703844877146E0725975
chr214487716244877224E0726099
chr214487728044877330E0726217
chr214487735344877434E0726290
chr214487745044877520E0726387
chr214488351144883785E07212448
chr214488387244884287E07212809
chr214488705844887532E07215995
chr214488781344888006E07216750
chr214488807844888195E07217015
chr214491284544915184E07241782
chr214487003344870388E073-675
chr214487056244870647E073-416
chr214487100844871556E0730
chr214487229744872416E0731234
chr214487258544872667E0731522
chr214487272244872832E0731659
chr214487306944873133E0732006
chr214487315444873333E0732091
chr214487478744874841E0733724
chr214487492944875001E0733866
chr214487505444875119E0733991
chr214487515844875208E0734095
chr214487526644875406E0734203
chr214487552644875995E0734463
chr214487599744876095E0734934
chr214487642244877004E0735359
chr214487703844877146E0735975
chr214487716244877224E0736099
chr214487728044877330E0736217
chr214487735344877434E0736290
chr214487745044877520E0736387
chr214488280344883350E07311740
chr214488335544883457E07312292
chr214488351144883785E07312448
chr214489745244898430E07326389
chr214489858444898670E07327521
chr214488280344883350E07411740
chr214488387244884287E07412809
chr214489726544897401E07426202
chr214482160244821681E081-49382
chr214482170544822092E081-48971
chr214484682044851548E081-19515
chr214486255444863210E081-7853
chr214486334544863530E081-7533
chr214486364244863837E081-7226
chr214486393544864116E081-6947
chr214486414444864196E081-6867
chr214486423344864379E081-6684
chr214486441144864826E081-6237
chr214486732244867755E081-3308
chr214486777544867886E081-3177
chr214486861044868841E081-2222
chr214486892444868974E081-2089
chr214486909844869171E081-1892
chr214486919344869305E081-1758
chr214486930744869372E081-1691
chr214486953044869708E081-1355
chr214486974544869819E081-1244
chr214486987344869996E081-1067
chr214487003344870388E081-675
chr214487056244870647E081-416
chr214487075044870881E081-182
chr214487100844871556E0810
chr214487166344872284E081600
chr214487229744872416E0811234
chr214487258544872667E0811522
chr214487272244872832E0811659
chr214487306944873133E0812006
chr214487315444873333E0812091
chr214487355744873619E0812494
chr214487390444873961E0812841
chr214487398344874521E0812920
chr214487453444874715E0813471
chr214487472444874777E0813661
chr214487478744874841E0813724
chr214487492944875001E0813866
chr214487505444875119E0813991
chr214487515844875208E0814095
chr214487526644875406E0814203
chr214487552644875995E0814463
chr214487599744876095E0814934
chr214487613044876420E0815067
chr214487642244877004E0815359
chr214487703844877146E0815975
chr214487716244877224E0816099
chr214487728044877330E0816217
chr214487735344877434E0816290
chr214487745044877520E0816387
chr214488202144882454E08110958
chr214488256044882606E08111497
chr214488265144882713E08111588
chr214488280344883350E08111740
chr214488335544883457E08112292
chr214488351144883785E08112448
chr214488387244884287E08112809
chr214489575544895941E08124692
chr214489614344896193E08125080
chr214490596144906261E08134898
chr214490626344906472E08135200
chr214491524444915339E08144181
chr214491534844915501E08144285
chr214491553844915629E08144475
chr214491568544915813E08144622
chr214491581644916131E08144753
chr214484208144842205E082-28858
chr214484224144842480E082-28583
chr214484250444842809E082-28254
chr214485169444851869E082-19194
chr214486057144861538E082-9525
chr214486157444861664E082-9399
chr214486919344869305E082-1758
chr214486930744869372E082-1691
chr214486953044869708E082-1355
chr214486974544869819E082-1244
chr214486987344869996E082-1067
chr214487003344870388E082-675
chr214487056244870647E082-416
chr214487075044870881E082-182
chr214487100844871556E0820
chr214487166344872284E082600
chr214487229744872416E0821234
chr214487258544872667E0821522
chr214487272244872832E0821659
chr214487306944873133E0822006
chr214487315444873333E0822091
chr214487355744873619E0822494
chr214487390444873961E0822841
chr214487398344874521E0822920
chr214487472444874777E0823661
chr214487478744874841E0823724
chr214487492944875001E0823866
chr214487505444875119E0823991
chr214487515844875208E0824095
chr214487526644875406E0824203
chr214487552644875995E0824463
chr214487599744876095E0824934
chr214487735344877434E0826290
chr214487745044877520E0826387
chr214488202144882454E08210958
chr214488256044882606E08211497
chr214488265144882713E08211588
chr214488280344883350E08211740
chr214488335544883457E08212292
chr214488351144883785E08212448
chr214490540444905552E08234341
chr214490556744905621E08234504
chr214490569744905782E08234634
chr214490579344905843E08234730
chr214490596144906261E08234898
chr214490626344906472E08235200










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr214484548344846819E067-24244
chr214484379544845482E068-25581
chr214484548344846819E068-24244
chr214484548344846819E069-24244
chr214484379544845482E070-25581
chr214484548344846819E070-24244
chr214484379544845482E071-25581
chr214484548344846819E071-24244
chr214484379544845482E072-25581
chr214484548344846819E072-24244
chr214484379544845482E073-25581
chr214484548344846819E073-24244
chr214484548344846819E074-24244
chr214484379544845482E081-25581
chr214484379544845482E082-25581
chr214484548344846819E082-24244