rs5999108

Homo sapiens
T>C
LARGE : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0474 (14168/29856,GnomAD)
T==0483 (14087/29114,TOPMED)
T==0500 (2503/5008,1000G)
C=0360 (1387/3854,ALSPAC)
C=0358 (1328/3708,TWINSUK)
chr22:33805813 (GRCh38.p7) (22q12.3)
AD
GWASdb2
1   publication(s)
See rs on genome
148 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 22NC_000022.11:g.33805813T>C
GRCh37.p13 chr 22NC_000022.10:g.34201800T>C
LARGE1 RefSeqGeneNG_009929.2:g.119616A>G

Gene: LARGE, like-glycosyltransferase(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LARGE1 transcript variant 1NM_004737.4:c.N/AIntron Variant
LARGE1 transcript variant 2NM_133642.3:c.N/AIntron Variant
LARGE1 transcript variant X1XM_005261831.3:c.N/AIntron Variant
LARGE1 transcript variant X3XM_005261832.3:c.N/AIntron Variant
LARGE1 transcript variant X2XM_011530510.2:c.N/AIntron Variant
LARGE transcript variant X7XM_011530514.2:c.N/AIntron Variant
LARGE1 transcript variant X6XM_011530512.2:c.N/AGenic Upstream Transcript Variant
LARGE1 transcript variant X7XM_011530513.2:c.N/AGenic Upstream Transcript Variant
LARGE transcript variant X4XR_001755370.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.242C=0.758
1000GenomesAmericanSub694T=0.740C=0.260
1000GenomesEast AsianSub1008T=0.573C=0.427
1000GenomesEuropeSub1006T=0.637C=0.363
1000GenomesGlobalStudy-wide5008T=0.500C=0.500
1000GenomesSouth AsianSub978T=0.460C=0.540
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.640C=0.360
The Genome Aggregation DatabaseAfricanSub8708T=0.286C=0.714
The Genome Aggregation DatabaseAmericanSub824T=0.720C=0.280
The Genome Aggregation DatabaseEast AsianSub1612T=0.607C=0.393
The Genome Aggregation DatabaseEuropeSub18410T=0.619C=0.380
The Genome Aggregation DatabaseGlobalStudy-wide29856T=0.525C=0.474
The Genome Aggregation DatabaseOtherSub302T=0.700C=0.300
Trans-Omics for Precision MedicineGlobalStudy-wide29114T=0.483C=0.516
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.642C=0.358
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
rs59991080.000925alcohol dependence20201924

eQTL of rs5999108 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 rs5999108 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 )
chr223416719634167441E067-34359
chr223416753734167886E067-33914
chr223422103034221093E06719230
chr223422110834221297E06719308
chr223422152634221683E06719726
chr223422173134221851E06719931
chr223422189634222083E06720096
chr223422214934222320E06720349
chr223422765234227912E06725852
chr223422809434228308E06726294
chr223422836234228508E06726562
chr223423125834231620E06729458
chr223423191134231961E06730111
chr223423201734232067E06730217
chr223423207034232124E06730270
chr223424631234246567E06744512
chr223424897534249032E06747175
chr223424916234249212E06747362
chr223425064234251001E06748842
chr223416497734165229E068-36571
chr223416719634167441E068-34359
chr223416753734167886E068-33914
chr223418772934187803E068-13997
chr223418803934188099E068-13701
chr223418880034189262E068-12538
chr223418931934189743E068-12057
chr223419000234190250E068-11550
chr223419038434190523E068-11277
chr223420342234203472E0681622
chr223420359034203717E0681790
chr223420413034204270E0682330
chr223420435134204424E0682551
chr223420452434204584E0682724
chr223422636034226476E06824560
chr223422667734226727E06824877
chr223422689434226944E06825094
chr223422697034227020E06825170
chr223422703834227098E06825238
chr223422721034227525E06825410
chr223422765234227912E06825852
chr223422809434228308E06826294
chr223422836234228508E06826562
chr223422866634228831E06826866
chr223422892734229044E06827127
chr223424665934247892E06844859
chr223424916234249212E06847362
chr223425064234251001E06848842
chr223422103034221093E06919230
chr223422110834221297E06919308
chr223422152634221683E06919726
chr223422173134221851E06919931
chr223422836234228508E06926562
chr223422866634228831E06926866
chr223422892734229044E06927127
chr223423229934232499E06930499
chr223423253834232647E06930738
chr223424665934247892E06944859
chr223424795034248323E06946150
chr223424841334248453E06946613
chr223424916234249212E06947362
chr223425064234251001E06948842
chr223420475334204883E0702953
chr223421160534211705E0709805
chr223421175934211839E0709959
chr223424665934247892E07044859
chr223424795034248323E07046150
chr223424916234249212E07047362
chr223425064234251001E07048842
chr223418126434182006E071-19794
chr223418931934189743E071-12057
chr223422615334226251E07124353
chr223422636034226476E07124560
chr223422809434228308E07126294
chr223422836234228508E07126562
chr223422866634228831E07126866
chr223422892734229044E07127127
chr223423112234231219E07129322
chr223423125834231620E07129458
chr223423191134231961E07130111
chr223423201734232067E07130217
chr223423207034232124E07130270
chr223423229934232499E07130499
chr223423253834232647E07130738
chr223425064234251001E07148842
chr223416719634167441E072-34359
chr223416753734167886E072-33914
chr223418126434182006E072-19794
chr223422103034221093E07219230
chr223422110834221297E07219308
chr223422765234227912E07225852
chr223422809434228308E07226294
chr223422836234228508E07226562
chr223422866634228831E07226866
chr223423125834231620E07229458
chr223424795034248323E07246150
chr223424916234249212E07247362
chr223415303734153150E073-48650
chr223417282134172895E073-28905
chr223417296134173192E073-28608
chr223417326734173472E073-28328
chr223423125834231620E07329458
chr223423191134231961E07330111
chr223423201734232067E07330217
chr223423207034232124E07330270
chr223424665934247892E07344859
chr223424897534249032E07347175
chr223424916234249212E07347362
chr223421933734219861E07417537
chr223422836234228508E07426562
chr223422866634228831E07426866
chr223424897534249032E07447175
chr223424916234249212E07447362
chr223425064234251001E07448842
chr223415594734155997E081-45803
chr223415609334156163E081-45637
chr223415620634156334E081-45466
chr223416719634167441E081-34359
chr223416753734167886E081-33914
chr223416796134168011E081-33789
chr223418126434182006E081-19794
chr223418202834182088E081-19712
chr223418211134182163E081-19637
chr223421311434213215E08111314
chr223422601034226131E08124210
chr223422615334226251E08124353
chr223422765234227912E08125852
chr223422809434228308E08126294
chr223422836234228508E08126562
chr223423095434231004E08129154
chr223423112234231219E08129322
chr223423125834231620E08129458
chr223423191134231961E08130111
chr223423201734232067E08130217
chr223423207034232124E08130270
chr223423290334233169E08131103
chr223423331634233588E08131516
chr223423362734233867E08131827
chr223424897534249032E08147175
chr223424916234249212E08147362
chr223416895134169240E082-32560
chr223416929234169491E082-32309
chr223418243434182484E082-19316
chr223423095434231004E08229154
chr223423112234231219E08229322
chr223423125834231620E08229458
chr223423191134231961E08230111
chr223423201734232067E08230217
chr223423207034232124E08230270










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr223424929034250201E06747490
chr223424929034250201E06847490
chr223424929034250201E06947490
chr223424929034250201E07047490
chr223424929034250201E07147490
chr223424929034250201E07247490
chr223424929034250201E07347490
chr223424929034250201E07447490
chr223424929034250201E08247490