rs11779629

Homo sapiens
A>T
CSGALNACT1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0031 (950/29990,GnomAD)
T=0027 (798/29118,TOPMED)
T=0010 (49/5008,1000G)
T=0045 (173/3854,ALSPAC)
T=0044 (163/3708,TWINSUK)
chr8:19654461 (GRCh38.p7) (8p21.3)
AD
GWASdb2
1   publication(s)
See rs on genome
217 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 8NC_000008.11:g.19654461A>T
GRCh37.p13 chr 8NC_000008.10:g.19511972A>T

Gene: CSGALNACT1, chondroitin sulfate N-acetylgalactosaminyltransferase 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CSGALNACT1 transcript variant 2NM_018371.4:c.N/AIntron Variant
CSGALNACT1 transcript variant 1NM_001130518.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant 3NR_024040.1:n.N/AIntron Variant
CSGALNACT1 transcript variant X16XM_006716362.2:c.N/AIntron Variant
CSGALNACT1 transcript variant X3XM_006716363.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X16XM_011544584.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X17XM_017013626.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X17XM_017013627.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X19XM_017013628.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X18XM_017013629.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X21XM_017013630.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X22XM_017013631.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X23XM_017013632.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X24XM_017013633.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X25XM_017013634.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X26XM_017013635.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X27XM_017013636.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X28XM_017013637.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X19XM_017013638.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X1XM_006716358.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X3XM_006716359.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X7XM_006716360.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X10XM_006716361.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X14XM_006716364.3:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X4XM_011544578.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X5XM_011544579.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X8XM_011544580.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X9XM_011544582.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X15XM_011544583.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X36XM_011544585.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X6XM_017013623.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X11XM_017013624.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X13XM_017013625.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X35XM_017013639.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X31XR_001745561.1:n.N/AIntron Variant
CSGALNACT1 transcript variant X33XR_001745563.1:n.N/AIntron Variant
CSGALNACT1 transcript variant X34XR_001745564.1:n.N/AIntron Variant
CSGALNACT1 transcript variant X30XR_001745560.1:n.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X32XR_001745562.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.998T=0.002
1000GenomesAmericanSub694A=0.990T=0.010
1000GenomesEast AsianSub1008A=1.000T=0.000
1000GenomesEuropeSub1006A=0.971T=0.029
1000GenomesGlobalStudy-wide5008A=0.990T=0.010
1000GenomesSouth AsianSub978A=0.990T=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.955T=0.045
The Genome Aggregation DatabaseAfricanSub8732A=0.991T=0.009
The Genome Aggregation DatabaseAmericanSub838A=0.990T=0.010
The Genome Aggregation DatabaseEast AsianSub1618A=1.000T=0.000
The Genome Aggregation DatabaseEuropeSub18500A=0.954T=0.046
The Genome Aggregation DatabaseGlobalStudy-wide29990A=0.968T=0.031
The Genome Aggregation DatabaseOtherSub302A=0.970T=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.972T=0.027
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.956T=0.044
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
rs117796293.55E-05alcohol dependence21314694

eQTL of rs11779629 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 rs11779629 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 )
chr81949646419497287E067-14685
chr81950006619500146E067-11826
chr81950272219502855E067-9117
chr81950291619503126E067-8846
chr81950316719503427E067-8545
chr81950434319504444E067-7528
chr81950464519504755E067-7217
chr81950502419505127E067-6845
chr81950541219505565E067-6407
chr81950557119505795E067-6177
chr81951916419519275E0677192
chr81952863219528703E06716660
chr81953081519530865E06718843
chr81953087719530972E06718905
chr81953100519531066E06719033
chr81953107519531125E06719103
chr81953912619541051E06727154
chr81946496919465672E068-46300
chr81946569019465864E068-46108
chr81948165919481699E068-30273
chr81949569119496152E068-15820
chr81949624719496418E068-15554
chr81949646419497287E068-14685
chr81949934119500059E068-11913
chr81950006619500146E068-11826
chr81950272219502855E068-9117
chr81950291619503126E068-8846
chr81950316719503427E068-8545
chr81950372419503835E068-8137
chr81950399619504058E068-7914
chr81950502419505127E068-6845
chr81950541219505565E068-6407
chr81950557119505795E068-6177
chr81950582219505872E068-6100
chr81953856919538668E06826597
chr81954818819548248E06836216
chr81954847419548540E06836502
chr81954868119548935E06836709
chr81954897319549362E06837001
chr81955478419554863E06842812
chr81946459619464795E069-47177
chr81946485719464938E069-47034
chr81946496919465672E069-46300
chr81946569019465864E069-46108
chr81949514619495676E069-16296
chr81949569119496152E069-15820
chr81949624719496418E069-15554
chr81949646419497287E069-14685
chr81949922319499273E069-12699
chr81949934119500059E069-11913
chr81950006619500146E069-11826
chr81950272219502855E069-9117
chr81950291619503126E069-8846
chr81950316719503427E069-8545
chr81950434319504444E069-7528
chr81950464519504755E069-7217
chr81950502419505127E069-6845
chr81950541219505565E069-6407
chr81950557119505795E069-6177
chr81950582219505872E069-6100
chr81952013519520691E0698163
chr81952729519527723E06915323
chr81955217519552237E06940203
chr81955246719552756E06940495
chr81955478419554863E06942812
chr81946496919465672E070-46300
chr81950434319504444E070-7528
chr81950464519504755E070-7217
chr81950541219505565E070-6407
chr81946485719464938E071-47034
chr81946496919465672E071-46300
chr81946569019465864E071-46108
chr81949569119496152E071-15820
chr81949624719496418E071-15554
chr81949646419497287E071-14685
chr81949743419497627E071-14345
chr81949896519499063E071-12909
chr81949922319499273E071-12699
chr81949934119500059E071-11913
chr81950128519501498E071-10474
chr81950221719502356E071-9616
chr81950272219502855E071-9117
chr81950291619503126E071-8846
chr81950316719503427E071-8545
chr81950541219505565E071-6407
chr81950557119505795E071-6177
chr81950582219505872E071-6100
chr81952013519520691E0718163
chr81953856919538668E07126597
chr81955478419554863E07142812
chr81955490319555005E07142931
chr81946569019465864E072-46108
chr81946998019470257E072-41715
chr81949569119496152E072-15820
chr81949624719496418E072-15554
chr81949646419497287E072-14685
chr81949743419497627E072-14345
chr81949922319499273E072-12699
chr81949934119500059E072-11913
chr81950006619500146E072-11826
chr81950272219502855E072-9117
chr81950291619503126E072-8846
chr81950316719503427E072-8545
chr81950372419503835E072-8137
chr81950399619504058E072-7914
chr81950434319504444E072-7528
chr81950464519504755E072-7217
chr81950502419505127E072-6845
chr81950541219505565E072-6407
chr81950557119505795E072-6177
chr81952013519520691E0728163
chr81952863219528703E07216660
chr81953912619541051E07227154
chr81954868119548935E07236709
chr81954897319549362E07237001
chr81954991719550003E07237945
chr81955009719550147E07238125
chr81955017219550212E07238200
chr81955031919550776E07238347
chr81946301019463174E073-48798
chr81946330519463386E073-48586
chr81946339719463525E073-48447
chr81946496919465672E073-46300
chr81946569019465864E073-46108
chr81946590319466610E073-45362
chr81949624719496418E073-15554
chr81949896519499063E073-12909
chr81949922319499273E073-12699
chr81949934119500059E073-11913
chr81950272219502855E073-9117
chr81950291619503126E073-8846
chr81950316719503427E073-8545
chr81951097319511034E073-938
chr81951118819511251E073-721
chr81951133019511390E073-582
chr81951144319511969E073-3
chr81952013519520691E0738163
chr81952077619520849E0738804
chr81954868119548935E07336709
chr81954897319549362E07337001
chr81955217519552237E07340203
chr81955246719552756E07340495
chr81946485719464938E074-47034
chr81946496919465672E074-46300
chr81947170419471805E074-40167
chr81947185419471982E074-39990
chr81947218819472438E074-39534
chr81948248919482638E074-29334
chr81948269519482775E074-29197
chr81948314219483401E074-28571
chr81949514619495676E074-16296
chr81949569119496152E074-15820
chr81949624719496418E074-15554
chr81949646419497287E074-14685
chr81949743419497627E074-14345
chr81949922319499273E074-12699
chr81949934119500059E074-11913
chr81950006619500146E074-11826
chr81950108219501134E074-10838
chr81950128519501498E074-10474
chr81950221719502356E074-9616
chr81950272219502855E074-9117
chr81950291619503126E074-8846
chr81950316719503427E074-8545
chr81950372419503835E074-8137
chr81950399619504058E074-7914
chr81950434319504444E074-7528
chr81950464519504755E074-7217
chr81950502419505127E074-6845
chr81950541219505565E074-6407
chr81950557119505795E074-6177
chr81950582219505872E074-6100
chr81955353219554772E07441560
chr81955478419554863E07442812
chr81946459619464795E081-47177
chr81946485719464938E081-47034
chr81946496919465672E081-46300
chr81946569019465864E081-46108
chr81949855119498622E081-13350
chr81949868819498887E081-13085
chr81949896519499063E081-12909
chr81949922319499273E081-12699
chr81949934119500059E081-11913
chr81952094619521972E0818974
chr81952204219522122E08110070
chr81952219619524217E08110224
chr81952822119528603E08116249
chr81952863219528703E08116660
chr81954204219542092E08130070
chr81954215119542211E08130179
chr81954225319542358E08130281
chr81955123319551334E08139261
chr81955133619551386E08139364
chr81955139519551596E08139423
chr81955164319552109E08139671
chr81955217519552237E08140203
chr81955246719552756E08140495
chr81955276319552883E08140791
chr81955290319553082E08140931
chr81955310219553524E08141130
chr81955353219554772E08141560
chr81955490319555005E08142931
chr81946569019465864E082-46108
chr81948887219488934E082-23038
chr81948912619489417E082-22555
chr81948949119489686E082-22286
chr81948970519490365E082-21607
chr81952982519529894E08217853
chr81953912619541051E08227154
chr81954204219542092E08230070
chr81955164319552109E08239671
chr81955217519552237E08240203
chr81955246719552756E08240495
chr81955478419554863E08242812
chr81955490319555005E08242931
chr81955506319555686E08243091
chr81955576019555827E08243788