rs2554840

Homo sapiens
A>G
LOC105372211 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0369 (11066/29926,GnomAD)
G=0351 (10241/29118,TOPMED)
G=0333 (1668/5008,1000G)
G=0400 (1543/3854,ALSPAC)
G=0405 (1503/3708,TWINSUK)
chr18:76316449 (GRCh38.p7) (18q23)
AD
GWASdb2
1   publication(s)
See rs on genome
40 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 18NC_000018.10:g.76316449A>G
GRCh37.p13 chr 18NC_000018.9:g.74028404A>G

Gene: LOC105372211, uncharacterized LOC105372211(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105372211 transcriptXR_935655.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.659G=0.341
1000GenomesAmericanSub694A=0.720G=0.280
1000GenomesEast AsianSub1008A=0.725G=0.275
1000GenomesEuropeSub1006A=0.584G=0.416
1000GenomesGlobalStudy-wide5008A=0.667G=0.333
1000GenomesSouth AsianSub978A=0.660G=0.340
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.600G=0.400
The Genome Aggregation DatabaseAfricanSub8704A=0.658G=0.342
The Genome Aggregation DatabaseAmericanSub838A=0.770G=0.230
The Genome Aggregation DatabaseEast AsianSub1622A=0.753G=0.247
The Genome Aggregation DatabaseEuropeSub18460A=0.600G=0.399
The Genome Aggregation DatabaseGlobalStudy-wide29926A=0.630G=0.369
The Genome Aggregation DatabaseOtherSub302A=0.600G=0.400
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.648G=0.351
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.595G=0.405
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
rs25548400.000949alcohol dependence20201924

eQTL of rs2554840 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 rs2554840 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 )
chr187407064074070698E06742236
chr187406012474060209E06931720
chr187398652873987050E070-41354
chr187398968373989733E070-38671
chr187398975473990262E070-38142
chr187406012474060209E07031720
chr187407413674074204E07045732
chr187407438674074457E07045982
chr187407521874075904E07046814
chr187407591074076216E07047506
chr187407680874077198E07048404
chr187407723774077350E07048833
chr187407739874077580E07048994
chr187407768474077802E07049280
chr187407827874078365E07049874
chr187398652873987050E081-41354
chr187398968373989733E081-38671
chr187398975473990262E081-38142
chr187406012474060209E08131720
chr187406030574061708E08131901
chr187406365074064741E08135246
chr187407064074070698E08142236
chr187407105974071140E08142655
chr187407155874071626E08143154
chr187407413674074204E08145732
chr187407438674074457E08145982
chr187407521874075904E08146814
chr187407591074076216E08147506
chr187407680874077198E08148404
chr187407723774077350E08148833
chr187407739874077580E08148994
chr187407768474077802E08149280
chr187398968373989733E082-38671
chr187398975473990262E082-38142
chr187406012474060209E08231720
chr187406030574061708E08231901
chr187407680874077198E08248404
chr187407723774077350E08248833
chr187407739874077580E08248994
chr187407768474077802E08249280