rs372540087

Homo sapiens
delAGA
LCP1 : Intron Variant
Check p-value
Indel (Insertion and Deletion)
delAGA=0004 (138/29116,TOPMED)
delAGA=0003 (14/5008,1000G)
chr13:46180600-46180605 (GRCh38.p7) (13q14.13)
AD
GWASdb2
1   publication(s)
See rs on genome
47 Enhancers around
12 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.46180600_46180602[1]
GRCh37.p13 chr 13NC_000013.10:g.46754735_46754737[1]

Gene: LCP1, lymphocyte cytosolic protein 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LCP1 transcriptNM_002298.4:c.N/AIntron Variant
LCP1 transcript variant X1XM_005266374.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub2451(AGA)2=0.461delAGA=0.461
1000GenomesAmericanSub1372(AGA)2=0.494delAGA=0.494
1000GenomesEast AsianSub1972(AGA)2=0.489delAGA=0.489
1000GenomesEuropeSub1988(AGA)2=0.494delAGA=0.494
1000GenomesGlobalStudy-wide5008(AGA)2=0.928delAGA=0.928
1000GenomesSouth AsianSub1873(AGA)2=0.478delAGA=0.478
Trans-Omics for Precision MedicineGlobalStudy-wide29116(AGA)2=0.995delAGA=0.004
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
rs3725400870.000193alcohol dependence20201924

eQTL of rs372540087 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 rs372540087 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 )
chr134678736046787427E06732625
chr134678749446787803E06732759
chr134671680346717336E068-37399
chr134671738046717536E068-37199
chr134671765846717819E068-36916
chr134671738046717536E069-37199
chr134673063046730684E069-24051
chr134673073446730914E069-23821
chr134671629346716423E070-38312
chr134671664846716698E070-38037
chr134671680346717336E070-37399
chr134671884546718931E070-35804
chr134671920446719254E070-35481
chr134671938346719437E070-35298
chr134676365546763727E0708920
chr134676411746764227E0709382
chr134676447346764523E0709738
chr134676458546764635E0709850
chr134676476446764804E07010029
chr134671738046717536E071-37199
chr134671765846717819E071-36916
chr134678198146782242E07127246
chr134678244946782489E07127714
chr134678249846782561E07127763
chr134671664846716698E072-38037
chr134671680346717336E072-37399
chr134671738046717536E072-37199
chr134671765846717819E072-36916
chr134671680346717336E074-37399
chr134671738046717536E074-37199
chr134671765846717819E074-36916
chr134672111946721352E074-33383
chr134672998246730046E074-24689
chr134678162146781805E07426886
chr134678187746781972E07427142
chr134678198146782242E07427246
chr134678244946782489E07427714
chr134678249846782561E07427763
chr134678261346782716E07427878
chr134671629346716423E081-38312
chr134671664846716698E081-38037
chr134671680346717336E081-37399
chr134671738046717536E081-37199
chr134671765846717819E081-36916
chr134671738046717536E082-37199
chr134671920446719254E082-35481
chr134671938346719437E082-35298









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr134678518246786567E06730447
chr134675187246752314E068-2421
chr134678518246786567E06830447
chr134678518246786567E06930447
chr134678518246786567E07030447
chr134675426246755796E0710
chr134678518246786567E07130447
chr134678518246786567E07230447
chr134678518246786567E07330447
chr134678518246786567E07430447
chr134678518246786567E08130447
chr134678518246786567E08230447