rs9990002

Homo sapiens
G>T
FAM19A1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0177 (5320/29928,GnomAD)
G==0243 (7100/29118,TOPMED)
G==0201 (1009/5008,1000G)
G==0062 (239/3854,ALSPAC)
G==0055 (204/3708,TWINSUK)
chr3:68116622 (GRCh38.p7) (3p14.1)
AD
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.68116622G>T
GRCh37.p13 chr 3NC_000003.11:g.68165772G>T

Gene: FAM19A1, family with sequence similarity 19 (chemokine (C-C motif)-like), member A1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
FAM19A1 transcript variant 2NM_001252216.1:c.N/AIntron Variant
FAM19A1 transcript variant 1NM_213609.3:c.N/AIntron Variant
FAM19A1 transcript variant X1XM_017006386.1:c.N/AIntron Variant
FAM19A1 transcript variant X2XM_017006387.1:c.N/AIntron Variant
FAM19A1 transcript variant X3XM_017006388.1:c.N/AIntron Variant
FAM19A1 transcript variant X4XM_017006389.1:c.N/AIntron Variant
FAM19A1 transcript variant X5XM_017006390.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.492T=0.508
1000GenomesAmericanSub694G=0.090T=0.910
1000GenomesEast AsianSub1008G=0.189T=0.811
1000GenomesEuropeSub1006G=0.070T=0.930
1000GenomesGlobalStudy-wide5008G=0.201T=0.799
1000GenomesSouth AsianSub978G=0.030T=0.970
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.062T=0.938
The Genome Aggregation DatabaseAfricanSub8692G=0.425T=0.575
The Genome Aggregation DatabaseAmericanSub836G=0.060T=0.940
The Genome Aggregation DatabaseEast AsianSub1616G=0.223T=0.777
The Genome Aggregation DatabaseEuropeSub18484G=0.063T=0.936
The Genome Aggregation DatabaseGlobalStudy-wide29928G=0.177T=0.822
The Genome Aggregation DatabaseOtherSub300G=0.110T=0.890
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.243T=0.756
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.055T=0.945
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
rs99900020.000352alcohol dependence20201924

eQTL of rs9990002 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 rs9990002 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 )
chr36819080468190860E07025032
chr36819138868192149E07025616
chr36817051768170754E0814745
chr36817143168171481E0815659
chr36818034168180392E08114569
chr36818338568183607E08117613
chr36818364568183813E08117873
chr36818509368185201E08119321
chr36818563668185938E08119864
chr36819080468190860E08125032
chr36819138868192149E08125616
chr36819318168193343E08127409
chr36819771568197857E08131943
chr36818078568180856E08215013