rs1672461

Homo sapiens
C>T
LOC105370792 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0382 (11428/29918,GnomAD)
C==0405 (11810/29118,TOPMED)
C==0349 (1750/5008,1000G)
C==0420 (1617/3854,ALSPAC)
C==0408 (1514/3708,TWINSUK)
chr15:41897998 (GRCh38.p7) (15q15.1)
AD
GWASdb2
1   publication(s)
See rs on genome
113 Enhancers around
2 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.41897998C>T
GRCh37.p13 chr 15NC_000015.9:g.42190196C>T

Gene: LOC105370792, uncharacterized LOC105370792(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105370792 transcriptNR_135681.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.448T=0.552
1000GenomesAmericanSub694C=0.290T=0.710
1000GenomesEast AsianSub1008C=0.085T=0.915
1000GenomesEuropeSub1006C=0.437T=0.563
1000GenomesGlobalStudy-wide5008C=0.349T=0.651
1000GenomesSouth AsianSub978C=0.440T=0.560
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.420T=0.580
The Genome Aggregation DatabaseAfricanSub8708C=0.411T=0.589
The Genome Aggregation DatabaseAmericanSub838C=0.290T=0.710
The Genome Aggregation DatabaseEast AsianSub1620C=0.077T=0.923
The Genome Aggregation DatabaseEuropeSub18450C=0.398T=0.601
The Genome Aggregation DatabaseGlobalStudy-wide29918C=0.382T=0.618
The Genome Aggregation DatabaseOtherSub302C=0.460T=0.540
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.405T=0.594
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.408T=0.592
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
rs16724610.000717alcohol dependence21314694

eQTL of rs1672461 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:42190196MAPKBP1ENSG00000137802.9C>T1.6567e-7123564Cerebellum
Chr15:42190196SPTBN5ENSG00000137877.8C>T2.3126e-167793Cerebellum
Chr15:42190196EHD4ENSG00000103966.5C>T9.1353e-17-74580Cerebellum
Chr15:42190196SPTBN5ENSG00000137877.8C>T1.4238e-57793Hypothalamus
Chr15:42190196SPTBN5ENSG00000137877.8C>T2.2860e-57793Cortex
Chr15:42190196SPTBN5ENSG00000137877.8C>T5.1172e-97793Cerebellar_Hemisphere
Chr15:42190196EHD4ENSG00000103966.5C>T4.3181e-11-74580Cerebellar_Hemisphere
Chr15:42190196SPTBN5ENSG00000137877.8C>T4.8044e-87793Caudate_basal_ganglia
Chr15:42190196SPTBN5ENSG00000137877.8C>T8.0474e-57793Hippocampus
Chr15:42190196SPTBN5ENSG00000137877.8C>T7.8598e-77793Substantia_nigra
Chr15:42190196SPTBN5ENSG00000137877.8C>T6.6494e-47793Putamen_basal_ganglia
Chr15:42190196SPTBN5ENSG00000137877.8C>T1.3713e-87793Nucleus_accumbens_basal_ganglia

meQTL of rs1672461 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 )
chr154219640142196530E0676205
chr154219653542197728E0676339
chr154220524542205538E06715049
chr154220560742205740E06715411
chr154220608042206307E06715884
chr154220635242206964E06716156
chr154220730442207413E06717108
chr154220838642208775E06718190
chr154220975142210616E06719555
chr154218613342186413E068-3783
chr154219653542197728E0686339
chr154220730442207413E06817108
chr154220757742207700E06817381
chr154220770142207844E06817505
chr154220788942207995E06817693
chr154220838642208775E06818190
chr154220975142210616E06819555
chr154221335942213718E06823163
chr154221371942214354E06823523
chr154222086642221907E06830670
chr154222227642223283E06832080
chr154223041242230535E06840216
chr154217517442176015E069-14181
chr154218646242187988E069-2208
chr154220524542205538E06915049
chr154220560742205740E06915411
chr154220757742207700E06917381
chr154220770142207844E06917505
chr154220788942207995E06917693
chr154220975142210616E06919555
chr154221371942214354E06923523
chr154222086642221907E06930670
chr154222884942230116E06938653
chr154217517442176015E071-14181
chr154218646242187988E071-2208
chr154219640142196530E0716205
chr154219653542197728E0716339
chr154220496242205103E07114766
chr154220511442205198E07114918
chr154220524542205538E07115049
chr154220560742205740E07115411
chr154220608042206307E07115884
chr154220635242206964E07116156
chr154220730442207413E07117108
chr154220757742207700E07117381
chr154220770142207844E07117505
chr154220788942207995E07117693
chr154220838642208775E07118190
chr154220975142210616E07119555
chr154221061742211458E07120421
chr154221148442212128E07121288
chr154221371942214354E07123523
chr154222086642221907E07130670
chr154222194542222112E07131749
chr154222227642223283E07132080
chr154222677742227594E07136581
chr154222778842227988E07137592
chr154222884942230116E07138653
chr154214585142145901E072-44295
chr154214593942146158E072-44038
chr154214617742146491E072-43705
chr154218646242187988E072-2208
chr154219653542197728E0726339
chr154220524542205538E07215049
chr154220560742205740E07215411
chr154220608042206307E07215884
chr154220635242206964E07216156
chr154220975142210616E07219555
chr154221061742211458E07220421
chr154221371942214354E07223523
chr154222086642221907E07230670
chr154222194542222112E07231749
chr154222212442222232E07231928
chr154218613342186413E073-3783
chr154219653542197728E0736339
chr154220608042206307E07315884
chr154220635242206964E07316156
chr154220730442207413E07317108
chr154220838642208775E07318190
chr154220880242209263E07318606
chr154220975142210616E07319555
chr154221061742211458E07320421
chr154221281042213310E07322614
chr154221335942213718E07323163
chr154221371942214354E07323523
chr154222086642221907E07330670
chr154222194542222112E07331749
chr154222212442222232E07331928
chr154222227642223283E07332080
chr154223777242237850E07347576
chr154223788242237940E07347686
chr154223796642238469E07347770
chr154220496242205103E07414766
chr154220511442205198E07414918
chr154220524542205538E07415049
chr154220560742205740E07415411
chr154220608042206307E07415884
chr154220635242206964E07416156
chr154220770142207844E07417505
chr154220788942207995E07417693
chr154220838642208775E07418190
chr154220880242209263E07418606
chr154220975142210616E07419555
chr154221335942213718E07423163
chr154221371942214354E07423523
chr154221437142214571E07424175
chr154222086642221907E07430670
chr154222227642223283E07432080
chr154218932842189511E081-685
chr154218963542190057E081-139
chr154219011842190226E0810
chr154222086642221907E08130670
chr154214593942146158E082-44038









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr154217441842174966E070-15230
chr154217441842174966E082-15230