rs7719717

Homo sapiens
T>G
GMCL1P1 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0221 (6639/29960,GnomAD)
T==0258 (7519/29118,TOPMED)
T==0187 (936/5008,1000G)
T==0145 (560/3854,ALSPAC)
T==0142 (526/3708,TWINSUK)
chr5:178185292 (GRCh38.p7) (5q35.3)
AD
GWASdb2
1   publication(s)
See rs on genome
93 Enhancers around
47 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.178185292T>G
GRCh37.p13 chr 5NC_000005.9:g.177612293T>G

Gene: GMCL1P1, germ cell-less, spermatogenesis associated 1 pseudogene 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
Non-protein-coding transcriptsNR_003281.1:n.214...NR_003281.1:n.2141A>CA>CNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.465G=0.535
1000GenomesAmericanSub694T=0.140G=0.860
1000GenomesEast AsianSub1008T=0.022G=0.978
1000GenomesEuropeSub1006T=0.128G=0.872
1000GenomesGlobalStudy-wide5008T=0.187G=0.813
1000GenomesSouth AsianSub978T=0.070G=0.930
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.145G=0.855
The Genome Aggregation DatabaseAfricanSub8706T=0.435G=0.565
The Genome Aggregation DatabaseAmericanSub838T=0.120G=0.880
The Genome Aggregation DatabaseEast AsianSub1620T=0.002G=0.998
The Genome Aggregation DatabaseEuropeSub18494T=0.146G=0.853
The Genome Aggregation DatabaseGlobalStudy-wide29960T=0.221G=0.778
The Genome Aggregation DatabaseOtherSub302T=0.100G=0.900
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.258G=0.741
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.142G=0.858
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
rs77197176.47E-05alcohol dependence21703634

eQTL of rs7719717 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 rs7719717 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 )
chr5177578833177578896E067-33397
chr5177579529177579619E067-32674
chr5177633799177634006E06721506
chr5177656761177656845E06744468
chr5177656884177656946E06744591
chr5177657023177657131E06744730
chr5177657264177657318E06744971
chr5177657405177657459E06745112
chr5177657660177657762E06745367
chr5177578395177578494E068-33799
chr5177578551177578723E068-33570
chr5177578833177578896E068-33397
chr5177579529177579619E068-32674
chr5177633799177634006E06821506
chr5177634057177634818E06821764
chr5177634826177634972E06822533
chr5177657660177657762E06845367
chr5177579529177579619E069-32674
chr5177633799177634006E06921506
chr5177634057177634818E06921764
chr5177656761177656845E06944468
chr5177656884177656946E06944591
chr5177657023177657131E06944730
chr5177657264177657318E06944971
chr5177657405177657459E06945112
chr5177657660177657762E06945367
chr5177578551177578723E070-33570
chr5177578833177578896E070-33397
chr5177634826177634972E07022533
chr5177635074177635315E07022781
chr5177637079177637188E07024786
chr5177657023177657131E07044730
chr5177657264177657318E07044971
chr5177657405177657459E07045112
chr5177657660177657762E07045367
chr5177576659177576847E071-35446
chr5177576911177576991E071-35302
chr5177577013177577087E071-35206
chr5177579529177579619E071-32674
chr5177633799177634006E07121506
chr5177634057177634818E07121764
chr5177640320177640394E07128027
chr5177640479177640559E07128186
chr5177656761177656845E07144468
chr5177656884177656946E07144591
chr5177657023177657131E07144730
chr5177657264177657318E07144971
chr5177657405177657459E07145112
chr5177657660177657762E07145367
chr5177579529177579619E072-32674
chr5177657023177657131E07244730
chr5177657264177657318E07244971
chr5177657405177657459E07245112
chr5177657660177657762E07245367
chr5177570584177570645E073-41648
chr5177570686177570797E073-41496
chr5177570931177571213E073-41080
chr5177578395177578494E073-33799
chr5177578551177578723E073-33570
chr5177578833177578896E073-33397
chr5177579529177579619E073-32674
chr5177633799177634006E07321506
chr5177634057177634818E07321764
chr5177634826177634972E07322533
chr5177635074177635315E07322781
chr5177635362177635454E07323069
chr5177635660177635854E07323367
chr5177657405177657459E07345112
chr5177657660177657762E07345367
chr5177578833177578896E074-33397
chr5177579529177579619E074-32674
chr5177581683177581747E074-30546
chr5177633799177634006E07421506
chr5177634057177634818E07421764
chr5177634826177634972E07422533
chr5177635074177635315E07422781
chr5177657023177657131E07444730
chr5177657264177657318E07444971
chr5177657405177657459E07445112
chr5177657660177657762E07445367
chr5177660594177660644E07448301
chr5177633799177634006E08121506
chr5177634057177634818E08121764
chr5177645989177646080E08133696
chr5177657023177657131E08144730
chr5177657264177657318E08144971
chr5177657405177657459E08145112
chr5177657660177657762E08145367
chr5177581683177581747E082-30546
chr5177634826177634972E08222533
chr5177635074177635315E08222781
chr5177657405177657459E08245112
chr5177657660177657762E08245367










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr5177580272177580431E067-31862
chr5177580579177581256E067-31037
chr5177581258177581342E067-30951
chr5177630843177632916E06718550
chr5177658763177660458E06746470
chr5177580272177580431E068-31862
chr5177580579177581256E068-31037
chr5177581258177581342E068-30951
chr5177630843177632916E06818550
chr5177658763177660458E06846470
chr5177580272177580431E069-31862
chr5177580579177581256E069-31037
chr5177581258177581342E069-30951
chr5177630843177632916E06918550
chr5177658763177660458E06946470
chr5177580272177580431E070-31862
chr5177580579177581256E070-31037
chr5177581258177581342E070-30951
chr5177630843177632916E07018550
chr5177658763177660458E07046470
chr5177580272177580431E071-31862
chr5177580579177581256E071-31037
chr5177581258177581342E071-30951
chr5177630843177632916E07118550
chr5177658763177660458E07146470
chr5177580272177580431E072-31862
chr5177580579177581256E072-31037
chr5177581258177581342E072-30951
chr5177630843177632916E07218550
chr5177658763177660458E07246470
chr5177580272177580431E073-31862
chr5177580579177581256E073-31037
chr5177581258177581342E073-30951
chr5177630843177632916E07318550
chr5177658763177660458E07346470
chr5177580272177580431E074-31862
chr5177580579177581256E074-31037
chr5177581258177581342E074-30951
chr5177630843177632916E07418550
chr5177658763177660458E07446470
chr5177580272177580431E081-31862
chr5177580579177581256E081-31037
chr5177580272177580431E082-31862
chr5177580579177581256E082-31037
chr5177581258177581342E082-30951
chr5177630843177632916E08218550
chr5177658763177660458E08246470