rs544475121

Homo sapiens
delT
LPAR6 : Intron Variant
RB1 : Intron Variant
Check p-value
Indel (Insertion and Deletion)
delT=0064 (323/5008,1000G)
chr13:48442207-48442218 (GRCh38.p7) (13q14.2)
AD
GWASCatalog
1   publication(s)
See rs on genome
19 Enhancers around
16 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.48442218delT
GRCh37.p13 chr 13NC_000013.10:g.49016354delT
RB1 RefSeqGene LRG_517
LPAR6 RefSeqGeneNG_012874.1:g.7498delA

Gene: RB1, retinoblastoma 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
RB1 transcriptNM_000321.2:c.N/AIntron Variant
RB1 transcript variant X1XM_011535171.2:c.N/AIntron Variant

Gene: LPAR6, lysophosphatidic acid receptor 6(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LPAR6 transcript variant 1NM_005767.5:c.N/AIntron Variant
LPAR6 transcript variant 2NM_001162497.1:c.N/AGenic Upstream Transcript Variant
LPAR6 transcript variant 3NM_001162498.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322(T)12=0.791delT=0.209
1000GenomesAmericanSub694(T)12=0.970delT=0.030
1000GenomesEast AsianSub1008(T)12=0.994delT=0.006
1000GenomesEuropeSub1006(T)12=0.988delT=0.012
1000GenomesGlobalStudy-wide5008(T)12=0.936delT=0.064
1000GenomesSouth AsianSub978(T)12=0.990delT=0.010
PMID Title Author Journal
29071344Genetic Risk Variants Associated With Comorbid Alcohol Dependence and Major Depression.Zhou HJAMA Psychiatry

P-Value

SNP ID p-value Traits Study
rs5444751215E-06alcohol dependence29071344

eQTL of rs544475121 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 rs544475121 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 )
chr134900620749006729E067-9625
chr134900674749006857E067-9497
chr134897439848974728E068-41626
chr134898172748981800E068-34554
chr134900620749006729E068-9625
chr134901156149012020E068-4334
chr134902286149023447E0686507
chr134902345349023555E0687099
chr134900554149006023E069-10331
chr134900620749006729E069-9625
chr134900674749006857E069-9497
chr134897480148974895E071-41459
chr134897494248975539E071-40815
chr134900554149006023E071-10331
chr134900620749006729E071-9625
chr134900554149006023E074-10331
chr134900620749006729E074-9625
chr134900674749006857E074-9497
chr134901090149011231E074-5123





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr134898526348987759E067-28595
chr134898345248983638E068-32716
chr134898416848985071E068-31283
chr134898526348987759E068-28595
chr134898416848985071E069-31283
chr134898526348987759E069-28595
chr134898345248983638E071-32716
chr134898416848985071E071-31283
chr134898526348987759E071-28595
chr134898416848985071E072-31283
chr134898526348987759E072-28595
chr134898416848985071E073-31283
chr134898526348987759E073-28595
chr134898416848985071E074-31283
chr134898526348987759E074-28595
chr134898526348987759E082-28595