rs6054627

Homo sapiens
A>G
SLC52A3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0242 (7242/29878,GnomAD)
A==0288 (8397/29118,TOPMED)
A==0296 (1480/5008,1000G)
A==0168 (648/3854,ALSPAC)
A==0171 (635/3708,TWINSUK)
chr20:767191 (GRCh38.p7) (20p13)
AD
GWASdb2
1   publication(s)
See rs on genome
48 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.767191A>G
GRCh37.p13 chr 20NC_000020.10:g.747835A>G
SLC52A3 RefSeqGeneNG_027687.1:g.6394T>C

Gene: SLC52A3, solute carrier family 52 member 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SLC52A3 transcriptNM_033409.3:c.N/AIntron Variant
SLC52A3 transcript variant X1XM_005260655.3:c.N/AIntron Variant
SLC52A3 transcript variant X3XM_011529148.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.433G=0.567
1000GenomesAmericanSub694A=0.270G=0.730
1000GenomesEast AsianSub1008A=0.267G=0.733
1000GenomesEuropeSub1006A=0.162G=0.838
1000GenomesGlobalStudy-wide5008A=0.296G=0.704
1000GenomesSouth AsianSub978A=0.300G=0.700
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.168G=0.832
The Genome Aggregation DatabaseAfricanSub8692A=0.400G=0.600
The Genome Aggregation DatabaseAmericanSub836A=0.210G=0.790
The Genome Aggregation DatabaseEast AsianSub1608A=0.249G=0.751
The Genome Aggregation DatabaseEuropeSub18440A=0.169G=0.830
The Genome Aggregation DatabaseGlobalStudy-wide29878A=0.242G=0.757
The Genome Aggregation DatabaseOtherSub302A=0.220G=0.780
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.288G=0.711
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.171G=0.829
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs60546270.000637alcohol dependence21314694

eQTL of rs6054627 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 rs6054627 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 )
chr20719366720307E067-27528
chr20698617698807E070-49028
chr20700472700822E070-47013
chr20700955701005E070-46830
chr20701025701150E070-46685
chr20701380701420E070-46415
chr20709673709755E070-38080
chr20714516714646E070-33189
chr20714675714740E070-33095
chr20714749714799E070-33036
chr20714947715045E070-32790
chr20719366720307E070-27528
chr20734511734576E070-13259
chr20734593734701E070-13134
chr20734732734874E070-12961
chr20734993735111E070-12724
chr20735195735249E070-12586
chr20719366720307E073-27528
chr20732458732743E073-15092
chr20732759732809E073-15026
chr20732862733188E073-14647
chr20700472700822E081-47013
chr20700955701005E081-46830
chr20701025701150E081-46685
chr20701380701420E081-46415
chr20703218703268E081-44567
chr20703410703567E081-44268
chr20703592703642E081-44193
chr20704311704361E081-43474
chr20704414704726E081-43109
chr20704765704869E081-42966
chr20707811707861E081-39974
chr20707923707973E081-39862
chr20714516714646E081-33189
chr20714675714740E081-33095
chr20714749714799E081-33036
chr20714947715045E081-32790
chr20734511734576E081-13259
chr20734593734701E081-13134
chr20699726699801E082-48034
chr20700472700822E082-47013
chr20700955701005E082-46830
chr20701025701150E082-46685
chr20704414704726E082-43109
chr20704765704869E082-42966
chr20704953705003E082-42832
chr20709673709755E082-38080
chr20741294741344E082-6491





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr20708581708830E067-39005
chr20708937709653E067-38182
chr20748591748715E067756
chr20748782748851E067947
chr20750826750950E0672991
chr20708581708830E068-39005
chr20708937709653E068-38182
chr20748591748715E068756
chr20748782748851E068947
chr20708581708830E069-39005
chr20708937709653E069-38182
chr20748591748715E069756
chr20748782748851E069947
chr20750826750950E0692991
chr20708474708525E070-39310
chr20708581708830E070-39005
chr20708937709653E070-38182
chr20708581708830E071-39005
chr20708937709653E071-38182
chr20708937709653E072-38182
chr20750826750950E0722991
chr20708581708830E073-39005
chr20708937709653E073-38182
chr20748591748715E073756
chr20748782748851E073947
chr20750826750950E0732991
chr20708474708525E082-39310
chr20708581708830E082-39005
chr20708937709653E082-38182