rs10083490

Homo sapiens
C>T
PLD4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0463 (13833/29872,GnomAD)
C==0446 (2234/5008,1000G)
C==0455 (1752/3854,ALSPAC)
C==0454 (1683/3708,TWINSUK)
chr14:104936081 (GRCh38.p7) (14q32.33)
AD
GWASdb2
1   publication(s)
See rs on genome
39 Enhancers around
13 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 14NC_000014.9:g.104936081C>T
GRCh37.p13 chr 14NC_000014.8:g.105402418C>T

Gene: PLD4, phospholipase D family member 4(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PLD4 transcript variant 1NM_001308174.1:c.N/AGenic Downstream Transcript Variant
PLD4 transcript variant 2NM_138790.3:c.N/AGenic Downstream Transcript Variant
PLD4 transcript variant X3XM_011536411.2:c.N/AIntron Variant
PLD4 transcript variant X4XM_017020965.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.360T=0.640
1000GenomesAmericanSub694C=0.490T=0.510
1000GenomesEast AsianSub1008C=0.589T=0.411
1000GenomesEuropeSub1006C=0.466T=0.534
1000GenomesGlobalStudy-wide5008C=0.446T=0.554
1000GenomesSouth AsianSub978C=0.360T=0.640
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.455T=0.545
The Genome Aggregation DatabaseAfricanSub8682C=0.360T=0.640
The Genome Aggregation DatabaseAmericanSub836C=0.480T=0.520
The Genome Aggregation DatabaseEast AsianSub1620C=0.560T=0.440
The Genome Aggregation DatabaseEuropeSub18432C=0.504T=0.495
The Genome Aggregation DatabaseGlobalStudy-wide29872C=0.463T=0.536
The Genome Aggregation DatabaseOtherSub302C=0.300T=0.700
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.454T=0.546
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs100834900.000695alcohol dependence21314694

eQTL of rs10083490 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr14:105402418C14orf79ENSG00000140104.9C>T2.1602e-15-49694Cerebellum
Chr14:105402418C14orf79ENSG00000140104.9C>T4.7616e-17-49694Cortex
Chr14:105402418C14orf79ENSG00000140104.9C>T6.9357e-18-49694Caudate_basal_ganglia

meQTL of rs10083490 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 )
chr14105441771105441859E06739353
chr14105448102105448873E06745684
chr14105448905105448995E06746487
chr14105433495105435865E06831077
chr14105438502105440901E06836084
chr14105440956105441087E06838538
chr14105362072105362574E070-39844
chr14105362595105363330E070-39088
chr14105438502105440901E07036084
chr14105440956105441087E07038538
chr14105448102105448873E07045684
chr14105394020105394079E071-8339
chr14105394143105394224E071-8194
chr14105432809105432863E07130391
chr14105433005105433073E07130587
chr14105448102105448873E07145684
chr14105394228105394338E072-8080
chr14105433495105435865E07231077
chr14105441771105441859E07239353
chr14105448102105448873E07245684
chr14105448905105448995E07246487
chr14105449041105449122E07246623
chr14105449133105449378E07246715
chr14105433495105435865E07331077
chr14105438502105440901E07336084
chr14105440956105441087E07338538
chr14105441178105441379E07338760
chr14105441405105441487E07338987
chr14105441505105441614E07339087
chr14105441625105441731E07339207
chr14105441771105441859E07339353
chr14105447864105448023E07345446
chr14105448102105448873E07345684
chr14105405819105405899E0743401
chr14105406110105406243E0743692
chr14105406357105406412E0743939
chr14105406557105406645E0744139
chr14105448102105448873E07445684
chr14105448905105448995E07446487







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr14105398766105398816E067-3602
chr14105398829105400089E067-2329
chr14105400148105400822E067-1596
chr14105398766105398816E068-3602
chr14105398829105400089E068-2329
chr14105398829105400089E069-2329
chr14105400148105400822E070-1596
chr14105398766105398816E071-3602
chr14105398829105400089E071-2329
chr14105398829105400089E072-2329
chr14105398766105398816E073-3602
chr14105398829105400089E073-2329
chr14105398829105400089E082-2329