rs10829622

Homo sapiens
T>C
MGMT : Intron Variant
LOC105378560 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0233 (6998/29986,GnomAD)
C=0238 (6930/29118,TOPMED)
C=0252 (1260/5008,1000G)
C=0276 (1065/3854,ALSPAC)
C=0269 (998/3708,TWINSUK)
chr10:129721248 (GRCh38.p7) (10q26.3)
AD
GWASdb2
1   publication(s)
See rs on genome
56 Enhancers around
4 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.129721248T>C
GRCh37.p13 chr 10NC_000010.10:g.131519512T>C

Gene: MGMT, O-6-methylguanine-DNA methyltransferase(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MGMT transcriptNM_002412.4:c.N/AIntron Variant
MGMT transcript variant X1XM_005252682.2:c.N/AIntron Variant
MGMT transcript variant X2XM_017016275.1:c.N/AIntron Variant

Gene: LOC105378560, uncharacterized LOC105378560(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105378560 transcriptXR_946467.2:n.111...XR_946467.2:n.11192T>CT>CNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.848C=0.152
1000GenomesAmericanSub694T=0.730C=0.270
1000GenomesEast AsianSub1008T=0.814C=0.186
1000GenomesEuropeSub1006T=0.725C=0.275
1000GenomesGlobalStudy-wide5008T=0.748C=0.252
1000GenomesSouth AsianSub978T=0.580C=0.420
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.724C=0.276
The Genome Aggregation DatabaseAfricanSub8728T=0.838C=0.162
The Genome Aggregation DatabaseAmericanSub836T=0.770C=0.230
The Genome Aggregation DatabaseEast AsianSub1618T=0.812C=0.188
The Genome Aggregation DatabaseEuropeSub18502T=0.730C=0.270
The Genome Aggregation DatabaseGlobalStudy-wide29986T=0.766C=0.233
The Genome Aggregation DatabaseOtherSub302T=0.690C=0.310
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.762C=0.238
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.731C=0.269
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
rs108296220.000458alcohol dependence21314694

eQTL of rs10829622 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 rs10829622 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 )
chr10131505956131506131E067-13381
chr10131476445131476485E068-43027
chr10131488981131489316E068-30196
chr10131489356131489468E068-30044
chr10131489587131489706E068-29806
chr10131556843131557203E06837331
chr10131557253131557308E06837741
chr10131557507131557717E06837995
chr10131505956131506131E069-13381
chr10131475894131475947E070-43565
chr10131476193131476260E070-43252
chr10131476311131476371E070-43141
chr10131476445131476485E070-43027
chr10131476602131476713E070-42799
chr10131483565131483654E070-35858
chr10131483963131484013E070-35499
chr10131506207131506909E070-12603
chr10131515077131515133E070-4379
chr10131556457131556539E07036945
chr10131556843131557203E07037331
chr10131557253131557308E07037741
chr10131557507131557717E07037995
chr10131557974131558093E07038462
chr10131558109131558163E07038597
chr10131488981131489316E071-30196
chr10131489356131489468E071-30044
chr10131489587131489706E071-29806
chr10131506207131506909E071-12603
chr10131557253131557308E07137741
chr10131560317131560470E07140805
chr10131505956131506131E072-13381
chr10131506207131506909E072-12603
chr10131492335131492754E073-26758
chr10131557253131557308E07337741
chr10131492335131492754E074-26758
chr10131560317131560470E07440805
chr10131560509131560635E07440997
chr10131503488131503668E081-15844
chr10131503794131503926E081-15586
chr10131506207131506909E081-12603
chr10131556457131556539E08136945
chr10131556843131557203E08137331
chr10131557253131557308E08137741
chr10131557507131557717E08137995
chr10131557974131558093E08138462
chr10131558109131558163E08138597
chr10131562853131562893E08143341
chr10131506207131506909E082-12603
chr10131556457131556539E08236945
chr10131556843131557203E08237331
chr10131557253131557308E08237741
chr10131557507131557717E08237995
chr10131557974131558093E08238462
chr10131565690131565740E08246178
chr10131565813131565863E08246301
chr10131566069131566113E08246557










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr10131555285131556088E06835773
chr10131555285131556088E06935773
chr10131555285131556088E07135773
chr10131555285131556088E07235773