rs11041553

Homo sapiens
G>A
LSP1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0027 (829/29918,GnomAD)
A=0029 (851/29118,TOPMED)
A=0059 (297/5008,1000G)
A=0023 (88/3854,ALSPAC)
A=0023 (84/3708,TWINSUK)
chr11:1867725 (GRCh38.p7) (11p15.5)
AD
GWASdb2
1   publication(s)
See rs on genome
62 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.1867725G>A
GRCh37.p13 chr 11NC_000011.9:g.1888955G>A
LSP1 RefSeqGeneNG_011509.1:g.19756G>A

Gene: LSP1, lymphocyte-specific protein 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LSP1 transcript variant 5NM_001242932.1:c.N/AIntron Variant
LSP1 transcript variant 1NM_002339.2:c.N/AIntron Variant
LSP1 transcript variant 2NM_001013253.1:c.N/AGenic Upstream Transcript Variant
LSP1 transcript variant 3NM_001013254.1:c.N/AGenic Upstream Transcript Variant
LSP1 transcript variant 4NM_001013255.1:c.N/AGenic Upstream Transcript Variant
LSP1 transcript variant 6NM_001289005.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.967A=0.033
1000GenomesAmericanSub694G=0.940A=0.060
1000GenomesEast AsianSub1008G=0.918A=0.082
1000GenomesEuropeSub1006G=0.977A=0.023
1000GenomesGlobalStudy-wide5008G=0.941A=0.059
1000GenomesSouth AsianSub978G=0.890A=0.110
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.977A=0.023
The Genome Aggregation DatabaseAfricanSub8708G=0.970A=0.030
The Genome Aggregation DatabaseAmericanSub836G=0.940A=0.060
The Genome Aggregation DatabaseEast AsianSub1622G=0.929A=0.071
The Genome Aggregation DatabaseEuropeSub18450G=0.978A=0.021
The Genome Aggregation DatabaseGlobalStudy-wide29918G=0.972A=0.027
The Genome Aggregation DatabaseOtherSub302G=0.950A=0.050
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.970A=0.029
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.977A=0.023
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
rs110415530.0000286alcoholismpha002891
rs110415530.0000286alcohol dependence20201924

eQTL of rs11041553 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 rs11041553 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 )
chr1118477661849199E067-39756
chr1118838671886458E067-2497
chr1118865241886652E067-2303
chr1118867291886814E067-2141
chr1118838671886458E068-2497
chr1118865241886652E068-2303
chr1118867291886814E068-2141
chr1118868731886920E068-2035
chr1118477661849199E069-39756
chr1118492551849305E069-39650
chr1118493351849395E069-39560
chr1118838671886458E069-2497
chr1118865241886652E069-2303
chr1118867291886814E069-2141
chr1118868731886920E069-2035
chr1118915491891638E0692594
chr1118477661849199E070-39756
chr1118838671886458E070-2497
chr1118865241886652E070-2303
chr1118477661849199E071-39756
chr1118492551849305E071-39650
chr1118493351849395E071-39560
chr1118495381849588E071-39367
chr1118496691849772E071-39183
chr1118498431849959E071-38996
chr1118607481861992E071-26963
chr1118838671886458E071-2497
chr1118865241886652E071-2303
chr1118867291886814E071-2141
chr1118868731886920E071-2035
chr1118870791887129E071-1826
chr1118872931887492E071-1463
chr1118973041898303E0718349
chr1118477661849199E072-39756
chr1118838671886458E072-2497
chr1118865241886652E072-2303
chr1118867291886814E072-2141
chr1118906781891052E0721723
chr1118911851891423E0722230
chr1118915491891638E0722594
chr1118927091892795E0723754
chr1118471781847228E073-41727
chr1118474771847550E073-41405
chr1118477661849199E073-39756
chr1118584921860302E073-28653
chr1118838671886458E073-2497
chr1118865241886652E073-2303
chr1118867291886814E073-2141
chr1118868731886920E073-2035
chr1118870791887129E073-1826
chr1118477661849199E074-39756
chr1118838671886458E074-2497
chr1118865241886652E074-2303
chr1118867291886814E074-2141
chr1118531561853306E081-35649
chr1118533131856480E081-32475
chr1118838671886458E081-2497
chr1118865241886652E081-2303
chr1118911851891423E0812230
chr1118915491891638E0812594
chr1118477661849199E082-39756
chr1118531561853306E082-35649