rs12911894

Homo sapiens
C>A
LRRK1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0118 (3543/29862,GnomAD)
A=0103 (3023/29118,TOPMED)
A=0086 (431/5008,1000G)
A=0117 (451/3854,ALSPAC)
A=0125 (465/3708,TWINSUK)
chr15:100953634 (GRCh38.p7) (15q26.3)
AD
GWASdb2
1   publication(s)
See rs on genome
9 Enhancers around
30 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.100953634C>A
GRCh37.p13 chr 15NC_000015.9:g.101493839C>A

Gene: LRRK1, leucine-rich repeat kinase 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LRRK1 transcriptNM_024652.4:c.N/AIntron Variant
LRRK1 transcript variant X1XM_011522012.2:c.N/AIntron Variant
LRRK1 transcript variant X2XM_011522013.2:c.N/AIntron Variant
LRRK1 transcript variant X3XM_011522014.2:c.N/AIntron Variant
LRRK1 transcript variant X5XM_011522016.2:c.N/AIntron Variant
LRRK1 transcript variant X11XM_011522019.2:c.N/AIntron Variant
LRRK1 transcript variant X9XM_005254979.3:c.N/AGenic Upstream Transcript Variant
LRRK1 transcript variant X4XM_011522015.2:c.N/AGenic Upstream Transcript Variant
LRRK1 transcript variant X8XM_011522017.2:c.N/AGenic Upstream Transcript Variant
LRRK1 transcript variant X10XM_011522018.2:c.N/AGenic Upstream Transcript Variant
LRRK1 transcript variant X6XM_017022570.1:c.N/AGenic Upstream Transcript Variant
LRRK1 transcript variant X7XR_931905.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.911A=0.089
1000GenomesAmericanSub694C=0.920A=0.080
1000GenomesEast AsianSub1008C=0.979A=0.021
1000GenomesEuropeSub1006C=0.860A=0.140
1000GenomesGlobalStudy-wide5008C=0.914A=0.086
1000GenomesSouth AsianSub978C=0.900A=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.883A=0.117
The Genome Aggregation DatabaseAfricanSub8696C=0.889A=0.111
The Genome Aggregation DatabaseAmericanSub834C=0.920A=0.080
The Genome Aggregation DatabaseEast AsianSub1618C=0.987A=0.013
The Genome Aggregation DatabaseEuropeSub18412C=0.866A=0.133
The Genome Aggregation DatabaseGlobalStudy-wide29862C=0.881A=0.118
The Genome Aggregation DatabaseOtherSub302C=0.900A=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.896A=0.103
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.875A=0.125
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
rs129118940.0003alcohol dependence(early age of onset)20201924
rs129118940.00095alcohol dependence20201924

eQTL of rs12911894 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 rs12911894 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 )
chr15101457644101457842E067-35997
chr15101462203101462253E067-31586
chr15101469639101470310E067-23529
chr15101470344101470440E067-23399
chr15101463457101463521E069-30318
chr15101468967101469017E070-24822
chr15101469108101469531E070-24308
chr15101460972101461137E072-32702
chr15101468543101468593E081-25246





Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr15101457964101460495E067-33344
chr15101513539101513651E06719700
chr15101513653101513845E06719814
chr15101513867101513982E06720028
chr15101514052101514409E06720213
chr15101457964101460495E068-33344
chr15101513279101513522E06819440
chr15101513539101513651E06819700
chr15101513653101513845E06819814
chr15101513867101513982E06820028
chr15101457964101460495E069-33344
chr15101513539101513651E06919700
chr15101513653101513845E06919814
chr15101513867101513982E06920028
chr15101457964101460495E071-33344
chr15101513279101513522E07119440
chr15101513539101513651E07119700
chr15101513653101513845E07119814
chr15101457964101460495E072-33344
chr15101513279101513522E07219440
chr15101513539101513651E07219700
chr15101513653101513845E07219814
chr15101514052101514409E07220213
chr15101457964101460495E073-33344
chr15101513279101513522E07319440
chr15101513539101513651E07319700
chr15101513653101513845E07319814
chr15101513867101513982E07320028
chr15101514052101514409E07320213
chr15101513867101513982E07420028