rs11546742

Homo sapiens
C>G
TUBB : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0021 (637/29980,GnomAD)
G=0017 (497/29118,TOPMED)
G=0008 (41/5008,1000G)
G=0032 (123/3854,ALSPAC)
G=0031 (116/3708,TWINSUK)
chr6:30724991 (GRCh38.p7) (6p21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
107 Enhancers around
78 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.30724991C>G
GRCh37.p13 chr 6NC_000006.11:g.30692768C>G
TUBB RefSeqGeneNG_034142.1:g.9791C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.2204730C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.2204836C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.2025777C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.2025075C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.1980104C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.1985700C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.2069066C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.2074651C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.2035242C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.2040862C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.1980841C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.1986426C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.2:g.2054494C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.1:g.2004410C>G

Gene: TUBB, tubulin beta class I(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TUBB transcript variant 1NM_001293212.1:c.N/A3 Prime UTR Variant
TUBB transcript variant 2NM_178014.3:c.N/A3 Prime UTR Variant
TUBB transcript variant 3NM_001293213.1:c.N/A3 Prime UTR Variant
TUBB transcript variant 4NM_001293214.1:c.N/A3 Prime UTR Variant
TUBB transcript variant 5NM_001293215.1:c.N/A3 Prime UTR Variant
TUBB transcript variant 6NM_001293216.1:c.N/A3 Prime UTR Variant
TUBB transcript variant 7NR_120608.1:n.163...NR_120608.1:n.1636C>GC>GNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.998G=0.002
1000GenomesAmericanSub694C=0.980G=0.020
1000GenomesEast AsianSub1008C=1.000G=0.000
1000GenomesEuropeSub1006C=0.975G=0.025
1000GenomesGlobalStudy-wide5008C=0.992G=0.008
1000GenomesSouth AsianSub978C=1.000G=0.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.968G=0.032
The Genome Aggregation DatabaseAfricanSub8728C=0.994G=0.006
The Genome Aggregation DatabaseAmericanSub836C=0.990G=0.010
The Genome Aggregation DatabaseEast AsianSub1620C=1.000G=0.000
The Genome Aggregation DatabaseEuropeSub18494C=0.969G=0.031
The Genome Aggregation DatabaseGlobalStudy-wide29980C=0.978G=0.021
The Genome Aggregation DatabaseOtherSub302C=0.990G=0.010
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.982G=0.017
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.969G=0.031
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
rs115467420.00012alcohol dependence(early age of onset)20201924
rs115467420.00036alcohol dependence20201924

eQTL of rs11546742 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 rs11546742 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 )
chr63064733130647646E067-45122
chr63064772330648016E067-44752
chr63064804030648227E067-44541
chr63064824630648343E067-44425
chr63068659430686665E067-6103
chr63068670130686781E067-5987
chr63070885030709106E06716082
chr63071929030719432E06726522
chr63073642730736602E06743659
chr63064772330648016E068-44752
chr63064804030648227E068-44541
chr63064824630648343E068-44425
chr63068648030686536E068-6232
chr63068659430686665E068-6103
chr63068670130686781E068-5987
chr63069077730690978E068-1790
chr63071929030719432E06826522
chr63071949330720797E06826725
chr63073127330732396E06838505
chr63073642730736602E06843659
chr63073663930738260E06843871
chr63064663730647246E069-45522
chr63064733130647646E069-45122
chr63068648030686536E069-6232
chr63068659430686665E069-6103
chr63068670130686781E069-5987
chr63069077730690978E069-1790
chr63070388130704025E06911113
chr63070415130704194E06911383
chr63070789930708037E06915131
chr63070806230708576E06915294
chr63070885030709106E06916082
chr63071949330720797E06926725
chr63073642730736602E06943659
chr63064663730647246E070-45522
chr63064733130647646E070-45122
chr63070885030709106E07016082
chr63071285230712973E07020084
chr63071301830713177E07020250
chr63071320030713296E07020432
chr63071336530713429E07020597
chr63065635330656751E071-36017
chr63070868130708779E07115913
chr63071949330720797E07126725
chr63072082330720890E07128055
chr63072097630721065E07128208
chr63072383530723889E07131067
chr63073127330732396E07138505
chr63073642730736602E07143659
chr63073663930738260E07143871
chr63064772330648016E072-44752
chr63064804030648227E072-44541
chr63064824630648343E072-44425
chr63073127330732396E07238505
chr63073663930738260E07243871
chr63064663730647246E073-45522
chr63064772330648016E073-44752
chr63069077730690978E073-1790
chr63069800430698048E0735236
chr63069809530698145E0735327
chr63069816830698276E0735400
chr63069846230698970E0735694
chr63070594730706007E07313179
chr63070608630706193E07313318
chr63070806230708576E07315294
chr63070868130708779E07315913
chr63070885030709106E07316082
chr63073127330732396E07338505
chr63073423130734643E07341463
chr63073642730736602E07343659
chr63073663930738260E07343871
chr63064733130647646E074-45122
chr63064772330648016E074-44752
chr63068648030686536E074-6232
chr63068659430686665E074-6103
chr63068670130686781E074-5987
chr63069077730690978E074-1790
chr63070885030709106E07416082
chr63071949330720797E07426725
chr63073127330732396E07438505
chr63064663730647246E081-45522
chr63064733130647646E081-45122
chr63064772330648016E081-44752
chr63064804030648227E081-44541
chr63064824630648343E081-44425
chr63065635330656751E081-36017
chr63065685030657058E081-35710
chr63065717830657279E081-35489
chr63068648030686536E081-6232
chr63068659430686665E081-6103
chr63068670130686781E081-5987
chr63069102330691114E081-1654
chr63069134830691798E081-970
chr63069185630692001E081-767
chr63069212930692212E081-556
chr63069239830692503E081-265
chr63069270730692787E0810
chr63069281830692911E08150
chr63069294630693241E081178
chr63069346330694162E081695
chr63070885030709106E08116082
chr63071285230712973E08120084
chr63065685030657058E082-35710
chr63065717830657279E082-35489
chr63068648030686536E082-6232
chr63068659430686665E082-6103
chr63068670130686781E082-5987










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63064958730651702E067-41066
chr63065176330652041E067-40727
chr63065211030652236E067-40532
chr63065224130652947E067-39821
chr63065298130656320E067-36448
chr63068462830685787E067-6981
chr63068709030689981E067-2787
chr63069002530690105E067-2663
chr63070924630712762E06716478
chr63064958730651702E068-41066
chr63065176330652041E068-40727
chr63065211030652236E068-40532
chr63065224130652947E068-39821
chr63065298130656320E068-36448
chr63068462830685787E068-6981
chr63068709030689981E068-2787
chr63069002530690105E068-2663
chr63070924630712762E06816478
chr63064958730651702E069-41066
chr63065176330652041E069-40727
chr63065211030652236E069-40532
chr63065224130652947E069-39821
chr63065298130656320E069-36448
chr63068462830685787E069-6981
chr63068709030689981E069-2787
chr63070924630712762E06916478
chr63064958730651702E070-41066
chr63065298130656320E070-36448
chr63068462830685787E070-6981
chr63068709030689981E070-2787
chr63070924630712762E07016478
chr63064958730651702E071-41066
chr63065176330652041E071-40727
chr63065211030652236E071-40532
chr63065224130652947E071-39821
chr63065298130656320E071-36448
chr63068462830685787E071-6981
chr63068709030689981E071-2787
chr63069002530690105E071-2663
chr63070924630712762E07116478
chr63064958730651702E072-41066
chr63065176330652041E072-40727
chr63065211030652236E072-40532
chr63065224130652947E072-39821
chr63065298130656320E072-36448
chr63068462830685787E072-6981
chr63068709030689981E072-2787
chr63069002530690105E072-2663
chr63070924630712762E07216478
chr63064958730651702E073-41066
chr63065176330652041E073-40727
chr63065211030652236E073-40532
chr63065224130652947E073-39821
chr63065298130656320E073-36448
chr63068462830685787E073-6981
chr63068709030689981E073-2787
chr63069002530690105E073-2663
chr63070924630712762E07316478
chr63064958730651702E074-41066
chr63065176330652041E074-40727
chr63065211030652236E074-40532
chr63065224130652947E074-39821
chr63065298130656320E074-36448
chr63068462830685787E074-6981
chr63068709030689981E074-2787
chr63069002530690105E074-2663
chr63070924630712762E07416478
chr63065176330652041E081-40727
chr63065211030652236E081-40532
chr63068462830685787E081-6981
chr63068709030689981E081-2787
chr63069002530690105E081-2663
chr63070924630712762E08116478
chr63065298130656320E082-36448
chr63068462830685787E082-6981
chr63068709030689981E082-2787
chr63069002530690105E082-2663
chr63070924630712762E08216478