rs6778524

Homo sapiens
T>C
PLCL2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0080 (2397/29936,GnomAD)
C=0127 (3715/29118,TOPMED)
C=0088 (442/5008,1000G)
C=0016 (61/3854,ALSPAC)
C=0018 (67/3708,TWINSUK)
chr3:16814451 (GRCh38.p7) (3p24.3)
AD
GWASdb2
1   publication(s)
See rs on genome
41 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.16814451T>C
GRCh37.p13 chr 3NC_000003.11:g.16855953T>C

Gene: PLCL2, phospholipase C like 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PLCL2 transcript variant 1NM_001144382.1:c.N/AGenic Upstream Transcript Variant
PLCL2 transcript variant 2NM_015184.5:c.N/AGenic Upstream Transcript Variant
PLCL2 transcript variant X2XM_017006023.1:c.N/AIntron Variant
PLCL2 transcript variant X4XM_006713073.3:c.N/AGenic Upstream Transcript Variant
PLCL2 transcript variant X1XM_017006022.1:c.N/AGenic Upstream Transcript Variant
PLCL2 transcript variant X3XM_017006024.1:c.N/AGenic Upstream Transcript Variant
PLCL2 transcript variant X5XM_017006025.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.722C=0.278
1000GenomesAmericanSub694T=0.960C=0.040
1000GenomesEast AsianSub1008T=1.000C=0.000
1000GenomesEuropeSub1006T=0.982C=0.018
1000GenomesGlobalStudy-wide5008T=0.912C=0.088
1000GenomesSouth AsianSub978T=0.970C=0.030
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.984C=0.016
The Genome Aggregation DatabaseAfricanSub8688T=0.760C=0.240
The Genome Aggregation DatabaseAmericanSub838T=0.970C=0.030
The Genome Aggregation DatabaseEast AsianSub1614T=0.999C=0.001
The Genome Aggregation DatabaseEuropeSub18494T=0.984C=0.015
The Genome Aggregation DatabaseGlobalStudy-wide29936T=0.919C=0.080
The Genome Aggregation DatabaseOtherSub302T=0.960C=0.040
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.872C=0.127
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.982C=0.018
PMID Title Author Journal
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology

P-Value

SNP ID p-value Traits Study
rs67785249E-08alcohol dependence21956439

eQTL of rs6778524 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 rs6778524 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 )
chr31688003716880407E06824084
chr31688046616880625E06824513
chr31689117416891748E06835221
chr31688003716880407E06924084
chr31688046616880625E06924513
chr31689117416891748E06935221
chr31684322516843681E070-12272
chr31685024116850503E070-5450
chr31685072216850781E070-5172
chr31688003716880407E07024084
chr31688046616880625E07024513
chr31688077216880822E07024819
chr31688087016881079E07024917
chr31688147816881549E07025525
chr31688984516889914E07033892
chr31689032716890379E07034374
chr31689044616890496E07034493
chr31683126616831532E071-24421
chr31684196816842208E071-13745
chr31687994116880035E07123988
chr31688003716880407E07124084
chr31689185016891910E07235897
chr31684322516843681E081-12272
chr31684379216843994E081-11959
chr31684400416844218E081-11735
chr31684426716844317E081-11636
chr31685024116850503E081-5450
chr31684274416843174E082-12779
chr31684322516843681E082-12272
chr31684379216843994E082-11959
chr31684400416844218E082-11735
chr31684426716844317E082-11636
chr31685194616852189E082-3764
chr31685221516852323E082-3630
chr31685255216852803E082-3150
chr31688003716880407E08224084
chr31688046616880625E08224513
chr31688077216880822E08224819
chr31689032716890379E08234374
chr31689044616890496E08234493
chr31689117416891748E08235221