rs10520754

Homo sapiens
C>T
MCTP2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0431 (12896/29868,GnomAD)
T=0435 (12679/29118,TOPMED)
T=0437 (2188/5008,1000G)
T=0401 (1547/3854,ALSPAC)
T=0409 (1518/3708,TWINSUK)
chr15:94416180 (GRCh38.p7) (15q26.2)
AD
GWASdb2
1   publication(s)
See rs on genome
53 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.94416180C>T
GRCh37.p13 chr 15NC_000015.9:g.94959409C>T

Gene: MCTP2, multiple C2 domains, transmembrane 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MCTP2 transcript variant 2NM_001159643.1:c.N/AIntron Variant
MCTP2 transcript variant 1NM_018349.3:c.N/AIntron Variant
MCTP2 transcript variant 3NM_001159644.1:c.N/AGenic Downstream Transcript Variant
MCTP2 transcript variant X4XM_005254955.3:c.N/AIntron Variant
MCTP2 transcript variant X15XM_005254960.2:c.N/AIntron Variant
MCTP2 transcript variant X5XM_006720603.2:c.N/AIntron Variant
MCTP2 transcript variant X3XM_011521770.1:c.N/AIntron Variant
MCTP2 transcript variant X6XM_011521771.2:c.N/AIntron Variant
MCTP2 transcript variant X7XM_011521772.2:c.N/AIntron Variant
MCTP2 transcript variant X14XM_011521775.2:c.N/AIntron Variant
MCTP2 transcript variant X1XM_017022403.1:c.N/AIntron Variant
MCTP2 transcript variant X9XM_017022404.1:c.N/AIntron Variant
MCTP2 transcript variant X10XM_017022405.1:c.N/AIntron Variant
MCTP2 transcript variant X8XM_011521773.2:c.N/AGenic Downstream Transcript Variant
MCTP2 transcript variant X11XM_011521774.2:c.N/AGenic Downstream Transcript Variant
MCTP2 transcript variant X2XR_931865.2:n.N/AIntron Variant
MCTP2 transcript variant X12XR_001751349.1:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.501T=0.499
1000GenomesAmericanSub694C=0.670T=0.330
1000GenomesEast AsianSub1008C=0.576T=0.424
1000GenomesEuropeSub1006C=0.540T=0.460
1000GenomesGlobalStudy-wide5008C=0.563T=0.437
1000GenomesSouth AsianSub978C=0.580T=0.420
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.599T=0.401
The Genome Aggregation DatabaseAfricanSub8706C=0.537T=0.463
The Genome Aggregation DatabaseAmericanSub836C=0.720T=0.280
The Genome Aggregation DatabaseEast AsianSub1606C=0.588T=0.412
The Genome Aggregation DatabaseEuropeSub18418C=0.575T=0.425
The Genome Aggregation DatabaseGlobalStudy-wide29868C=0.568T=0.431
The Genome Aggregation DatabaseOtherSub302C=0.530T=0.470
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.564T=0.435
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.591T=0.409
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
rs105207540.000719alcohol dependence20201924

eQTL of rs10520754 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 rs10520754 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 )
chr159490945394909569E070-49840
chr159491009294910315E070-49094
chr159491054394910603E070-48806
chr159491073794910827E070-48582
chr159491084994911548E070-47861
chr159491195494912004E070-47405
chr159491208694912255E070-47154
chr159491262194912676E070-46733
chr159491269194912751E070-46658
chr159491285494912935E070-46474
chr159491324194913384E070-46025
chr159491345794914101E070-45308
chr159491425194914441E070-44968
chr159491472494914774E070-44635
chr159491491094914951E070-44458
chr159495350594953637E070-5772
chr159495416794954259E070-5150
chr159495466394954763E070-4646
chr159495488094954930E070-4479
chr159495523294955370E070-4039
chr159495554494955634E070-3775
chr159495567294955764E070-3645
chr159495591094955991E070-3418
chr159495928294959977E0700
chr159496007894960378E070669
chr159496124594961483E0701836
chr159498652294986758E07027113
chr159498681994986869E07027410
chr159498687894986968E07027469
chr159491009294910315E081-49094
chr159491054394910603E081-48806
chr159491073794910827E081-48582
chr159491345794914101E081-45308
chr159495912694959211E081-198
chr159495928294959977E0810
chr159496007894960378E081669
chr159496124594961483E0811836
chr159496158094961640E0812171
chr159499355994993689E08134150
chr159499398194994739E08134572
chr159491009294910315E082-49094
chr159491054394910603E082-48806
chr159491073794910827E082-48582
chr159491084994911548E082-47861
chr159495815794958606E082-803
chr159495912694959211E082-198
chr159495928294959977E0820
chr159496007894960378E082669
chr159498575594986169E08226346
chr159498642694986476E08227017
chr159498652294986758E08227113
chr159498681994986869E08227410
chr159498687894986968E08227469