rs4842798

Homo sapiens
T>C
LOC105369901 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0274 (8222/29910,GnomAD)
C=0289 (8439/29118,TOPMED)
C=0264 (1322/5008,1000G)
C=0265 (1023/3854,ALSPAC)
C=0261 (966/3708,TWINSUK)
chr12:91931644 (GRCh38.p7) (12q21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.91931644T>C
GRCh37.p13 chr 12NC_000012.11:g.92325420T>C

Gene: LOC105369901, uncharacterized LOC105369901(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105369901 transcript variant X2XR_001749253.1:n.N/AIntron Variant
LOC105369901 transcript variant X3XR_001749254.1:n.N/AIntron Variant
LOC105369901 transcript variant X4XR_001749255.1:n.N/AIntron Variant
LOC105369901 transcript variant X5XR_001749256.1:n.N/AIntron Variant
LOC105369901 transcript variant X1XR_945202.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.651C=0.349
1000GenomesAmericanSub694T=0.650C=0.350
1000GenomesEast AsianSub1008T=0.923C=0.077
1000GenomesEuropeSub1006T=0.735C=0.265
1000GenomesGlobalStudy-wide5008T=0.736C=0.264
1000GenomesSouth AsianSub978T=0.720C=0.280
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.735C=0.265
The Genome Aggregation DatabaseAfricanSub8714T=0.665C=0.335
The Genome Aggregation DatabaseAmericanSub838T=0.660C=0.340
The Genome Aggregation DatabaseEast AsianSub1588T=0.908C=0.092
The Genome Aggregation DatabaseEuropeSub18468T=0.740C=0.259
The Genome Aggregation DatabaseGlobalStudy-wide29910T=0.725C=0.274
The Genome Aggregation DatabaseOtherSub302T=0.750C=0.250
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.710C=0.289
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.739C=0.261
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
rs48427980.0004alcohol dependence20201924

eQTL of rs4842798 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 rs4842798 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 )
chr129228522792285267E070-40153
chr129228561292285704E070-39716
chr129228576992286134E070-39286
chr129228620492286429E070-38991
chr129228649492286710E070-38710
chr129229048492291024E070-34396
chr129229110292291152E070-34268
chr129227813792278506E081-46914
chr129228576992286134E081-39286
chr129228620492286429E081-38991
chr129228649492286710E081-38710
chr129229110292291152E081-34268
chr129228576992286134E082-39286
chr129228620492286429E082-38991