rs9478099

Homo sapiens
G>C
TCTE3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0403 (12083/29938,GnomAD)
C=0418 (12182/29118,TOPMED)
G==0433 (2167/5008,1000G)
C=0268 (1034/3854,ALSPAC)
C=0261 (967/3708,TWINSUK)
chr6:169730151 (GRCh38.p7) (6q27)
AD
GWASdb2
1   publication(s)
See rs on genome
64 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.169730151G>C
GRCh37.p13 chr 6NC_000006.11:g.170130247G>C
GRCh38.p7 chr 6 alt locus HSCHR6_1_CTG4NT_187552.1:g.5353G>C

Gene: TCTE3, t-complex-associated-testis-expressed 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TCTE3 transcriptNM_174910.1:c.N/AGenic Downstream Transcript Variant
TCTE3 transcript variant X2XM_006715554.3:c.N/AIntron Variant
TCTE3 transcript variant X1XM_011536093.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.430C=0.570
1000GenomesAmericanSub694G=0.430C=0.570
1000GenomesEast AsianSub1008G=0.063C=0.937
1000GenomesEuropeSub1006G=0.693C=0.307
1000GenomesGlobalStudy-wide5008G=0.433C=0.567
1000GenomesSouth AsianSub978G=0.550C=0.450
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.732C=0.268
The Genome Aggregation DatabaseAfricanSub8712G=0.463C=0.537
The Genome Aggregation DatabaseAmericanSub836G=0.420C=0.580
The Genome Aggregation DatabaseEast AsianSub1620G=0.049C=0.951
The Genome Aggregation DatabaseEuropeSub18468G=0.714C=0.286
The Genome Aggregation DatabaseGlobalStudy-wide29938G=0.596C=0.403
The Genome Aggregation DatabaseOtherSub302G=0.680C=0.320
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.581C=0.418
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.739C=0.261
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
rs94780990.000808alcohol dependence21314694

eQTL of rs9478099 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:170130247ERMARDENSG00000130023.11G>C1.4473e-3-21471Cerebellum
Chr6:170130247WDR27ENSG00000184465.11G>C9.9141e-828088Cortex

meQTL of rs9478099 in Fetal Brain

Probe ID Position Gene beta p-value
cg15038512chr6:170123185PHF100.03948909397505275.0674e-12
cg24289452chr6:170231220-0.05181454506300783.8996e-9

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 )
chr6170103915170103990E067-26257
chr6170104454170104504E067-25743
chr6170104537170104616E067-25631
chr6170104662170104740E067-25507
chr6170105028170105094E067-25153
chr6170105127170105230E067-25017
chr6170105241170105293E067-24954
chr6170105375170105425E067-24822
chr6170153066170153137E06722819
chr6170153140170153446E06722893
chr6170100253170100340E068-29907
chr6170103915170103990E068-26257
chr6170122064170122118E069-8129
chr6170122347170122483E069-7764
chr6170103915170103990E070-26257
chr6170121413170121463E070-8784
chr6170121465170121572E070-8675
chr6170122064170122118E070-8129
chr6170122347170122483E070-7764
chr6170126864170126940E070-3307
chr6170126980170127076E070-3171
chr6170127170170127220E070-3027
chr6170127295170127393E070-2854
chr6170127456170127506E070-2741
chr6170127566170127619E070-2628
chr6170100253170100340E071-29907
chr6170103915170103990E071-26257
chr6170150212170150300E07119965
chr6170150346170150396E07120099
chr6170153066170153137E07122819
chr6170122064170122118E072-8129
chr6170122347170122483E072-7764
chr6170153066170153137E07222819
chr6170153140170153446E07222893
chr6170103915170103990E073-26257
chr6170104454170104504E073-25743
chr6170104537170104616E073-25631
chr6170104662170104740E073-25507
chr6170105028170105094E073-25153
chr6170105127170105230E073-25017
chr6170153066170153137E07322819
chr6170100253170100340E074-29907
chr6170103915170103990E074-26257
chr6170104454170104504E074-25743
chr6170153066170153137E07422819
chr6170100253170100340E081-29907
chr6170103915170103990E081-26257
chr6170104454170104504E081-25743
chr6170104537170104616E081-25631
chr6170106596170106719E081-23528
chr6170106964170107014E081-23233
chr6170122064170122118E081-8129
chr6170122347170122483E081-7764
chr6170176607170176678E08146360
chr6170100253170100340E082-29907
chr6170103915170103990E082-26257
chr6170105028170105094E082-25153
chr6170105127170105230E082-25017
chr6170105241170105293E082-24954
chr6170105375170105425E082-24822
chr6170150212170150300E08219965
chr6170150346170150396E08220099
chr6170153066170153137E08222819
chr6170153140170153446E08222893










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr6170101297170103503E067-26744
chr6170122646170126274E067-3973
chr6170150920170152921E06720673
chr6170101297170103503E068-26744
chr6170122646170126274E068-3973
chr6170150920170152921E06820673
chr6170101297170103503E069-26744
chr6170122646170126274E069-3973
chr6170150920170152921E06920673
chr6170101297170103503E070-26744
chr6170122646170126274E070-3973
chr6170150920170152921E07020673
chr6170101297170103503E071-26744
chr6170122646170126274E071-3973
chr6170150920170152921E07120673
chr6170101297170103503E072-26744
chr6170122646170126274E072-3973
chr6170150920170152921E07220673
chr6170101297170103503E073-26744
chr6170122646170126274E073-3973
chr6170150920170152921E07320673
chr6170101297170103503E074-26744
chr6170122646170126274E074-3973
chr6170150920170152921E07420673
chr6170101297170103503E081-26744
chr6170150920170152921E08120673
chr6170101297170103503E082-26744
chr6170122646170126274E082-3973
chr6170150920170152921E08220673