rs1392219

Homo sapiens
C>T
LINC00578 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0200 (6014/29942,GnomAD)
T=0182 (5319/29118,TOPMED)
T=0213 (1068/5008,1000G)
T=0201 (774/3854,ALSPAC)
T=0194 (720/3708,TWINSUK)
chr3:177504641 (GRCh38.p7) (3q26.32)
AD
GWASdb2
1   publication(s)
See rs on genome
180 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.177504641C>T
GRCh37.p13 chr 3NC_000003.11:g.177222429C>T

Gene: LINC00578, long intergenic non-protein coding RNA 578(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC00578 transcriptNR_047568.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.859T=0.141
1000GenomesAmericanSub694C=0.690T=0.310
1000GenomesEast AsianSub1008C=0.766T=0.234
1000GenomesEuropeSub1006C=0.802T=0.198
1000GenomesGlobalStudy-wide5008C=0.787T=0.213
1000GenomesSouth AsianSub978C=0.760T=0.240
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.799T=0.201
The Genome Aggregation DatabaseAfricanSub8722C=0.849T=0.151
The Genome Aggregation DatabaseAmericanSub836C=0.660T=0.340
The Genome Aggregation DatabaseEast AsianSub1616C=0.770T=0.230
The Genome Aggregation DatabaseEuropeSub18466C=0.782T=0.217
The Genome Aggregation DatabaseGlobalStudy-wide29942C=0.799T=0.200
The Genome Aggregation DatabaseOtherSub302C=0.920T=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.817T=0.182
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.806T=0.194
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs13922195E-06alcohol consumption23743675

eQTL of rs1392219 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 rs1392219 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 )
chr3177176986177177116E067-45313
chr3177177169177178271E067-44158
chr3177191013177191100E067-31329
chr3177191132177191248E067-31181
chr3177201004177201737E067-20692
chr3177207940177208037E067-14392
chr3177208077177208645E067-13784
chr3177208649177210059E067-12370
chr3177230846177232651E0678417
chr3177232659177232910E06710230
chr3177232963177233194E06710534
chr3177233347177233411E06710918
chr3177233716177234983E06711287
chr3177255609177255685E06733180
chr3177255823177257393E06733394
chr3177270894177271065E06748465
chr3177271566177271620E06749137
chr3177176986177177116E068-45313
chr3177177169177178271E068-44158
chr3177178426177178747E068-43682
chr3177181703177181943E068-40486
chr3177182060177182219E068-40210
chr3177182307177182393E068-40036
chr3177190006177190100E068-32329
chr3177194295177194480E068-27949
chr3177194532177194648E068-27781
chr3177199878177200548E068-21881
chr3177216079177216561E068-5868
chr3177230846177232651E0688417
chr3177232659177232910E06810230
chr3177232963177233194E06810534
chr3177233347177233411E06810918
chr3177233716177234983E06811287
chr3177248279177248329E06825850
chr3177248608177249131E06826179
chr3177249155177249270E06826726
chr3177254055177254242E06831626
chr3177255609177255685E06833180
chr3177255823177257393E06833394
chr3177270501177270569E06848072
chr3177270894177271065E06848465
chr3177271566177271620E06849137
chr3177176815177176865E069-45564
chr3177176867177176920E069-45509
chr3177176986177177116E069-45313
chr3177177169177178271E069-44158
chr3177199878177200548E069-21881
chr3177216079177216561E069-5868
chr3177230846177232651E0698417
chr3177232659177232910E06910230
chr3177232963177233194E06910534
chr3177233347177233411E06910918
chr3177233716177234983E06911287
chr3177254055177254242E06931626
chr3177254544177254667E06932115
chr3177254843177254964E06932414
chr3177255609177255685E06933180
chr3177255823177257393E06933394
chr3177269728177269768E06947299
chr3177270501177270569E06948072
chr3177270894177271065E06948465
chr3177271566177271620E06949137
chr3177177169177178271E070-44158
chr3177208077177208645E070-13784
chr3177208649177210059E070-12370
chr3177230846177232651E0708417
chr3177232659177232910E07010230
chr3177232963177233194E07010534
chr3177233347177233411E07010918
chr3177233716177234983E07011287
chr3177176815177176865E071-45564
chr3177176867177176920E071-45509
chr3177176986177177116E071-45313
chr3177177169177178271E071-44158
chr3177178426177178747E071-43682
chr3177182753177182930E071-39499
chr3177183044177183134E071-39295
chr3177183141177183314E071-39115
chr3177187986177188272E071-34157
chr3177190006177190100E071-32329
chr3177191013177191100E071-31329
chr3177191132177191248E071-31181
chr3177199878177200548E071-21881
chr3177201004177201737E071-20692
chr3177207940177208037E071-14392
chr3177217639177218016E071-4413
chr3177218090177218243E071-4186
chr3177230846177232651E0718417
chr3177232659177232910E07110230
chr3177232963177233194E07110534
chr3177233347177233411E07110918
chr3177233716177234983E07111287
chr3177247562177247755E07125133
chr3177248279177248329E07125850
chr3177254055177254242E07131626
chr3177254843177254964E07132414
chr3177255609177255685E07133180
chr3177255823177257393E07133394
chr3177269279177269572E07146850
chr3177269728177269768E07147299
chr3177270501177270569E07148072
chr3177270894177271065E07148465
chr3177271566177271620E07149137
chr3177176815177176865E072-45564
chr3177176867177176920E072-45509
chr3177176986177177116E072-45313
chr3177177169177178271E072-44158
chr3177207940177208037E072-14392
chr3177228605177228658E0726176
chr3177230846177232651E0728417
chr3177232659177232910E07210230
chr3177232963177233194E07210534
chr3177233716177234983E07211287
chr3177235047177235139E07212618
chr3177254055177254242E07231626
chr3177254544177254667E07232115
chr3177254843177254964E07232414
chr3177255609177255685E07233180
chr3177255823177257393E07233394
chr3177257478177257528E07235049
chr3177257552177257602E07235123
chr3177270501177270569E07248072
chr3177270894177271065E07248465
chr3177271566177271620E07249137
chr3177177169177178271E073-44158
chr3177191013177191100E073-31329
chr3177191132177191248E073-31181
chr3177207940177208037E073-14392
chr3177208077177208645E073-13784
chr3177208649177210059E073-12370
chr3177230846177232651E0738417
chr3177232659177232910E07310230
chr3177232963177233194E07310534
chr3177233347177233411E07310918
chr3177233716177234983E07311287
chr3177254843177254964E07332414
chr3177255609177255685E07333180
chr3177255823177257393E07333394
chr3177270894177271065E07348465
chr3177271566177271620E07349137
chr3177176815177176865E074-45564
chr3177176867177176920E074-45509
chr3177176986177177116E074-45313
chr3177177169177178271E074-44158
chr3177199228177199329E074-23100
chr3177199878177200548E074-21881
chr3177201004177201737E074-20692
chr3177206857177206925E074-15504
chr3177207940177208037E074-14392
chr3177208077177208645E074-13784
chr3177217639177218016E074-4413
chr3177218090177218243E074-4186
chr3177230846177232651E0748417
chr3177232659177232910E07410230
chr3177232963177233194E07410534
chr3177233347177233411E07410918
chr3177233716177234983E07411287
chr3177248608177249131E07426179
chr3177254843177254964E07432414
chr3177255609177255685E07433180
chr3177255823177257393E07433394
chr3177259512177259640E07437083
chr3177270501177270569E07448072
chr3177270894177271065E07448465
chr3177271566177271620E07449137
chr3177177169177178271E081-44158
chr3177208649177210059E081-12370
chr3177230846177232651E0818417
chr3177232659177232910E08110230
chr3177232963177233194E08110534
chr3177233347177233411E08110918
chr3177233716177234983E08111287
chr3177186176177186478E082-35951
chr3177208077177208645E082-13784
chr3177208649177210059E082-12370
chr3177232659177232910E08210230
chr3177232963177233194E08210534
chr3177233716177234983E08211287
chr3177255823177257393E08233394
chr3177257478177257528E08235049