rs17078678

Homo sapiens
C>A
SACS : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0040 (1215/29982,GnomAD)
A=0059 (1725/29116,TOPMED)
A=0047 (233/5008,1000G)
chr13:23383375 (GRCh38.p7) (13q12.12)
AD
GWASdb2
1   publication(s)
See rs on genome
209 Enhancers around
36 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.23383375C>A
GRCh37.p13 chr 13NC_000013.10:g.23957514C>A
SACS RefSeqGeneNG_012342.1:g.55328G>T

Gene: SACS, sacsin molecular chaperone(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SACS transcript variant 1NM_014363.5:c.N/AIntron Variant
SACS transcript variant 2NM_001278055.1:c.N/AGenic Upstream Transcript Variant
SACS transcript variant X1XM_005266338.2:c.N/AIntron Variant
SACS transcript variant X3XM_011535039.2:c.N/AGenic Upstream Transcript Variant
SACS transcript variant X4XM_017020539.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.834A=0.166
1000GenomesAmericanSub694C=0.980A=0.020
1000GenomesEast AsianSub1008C=1.000A=0.000
1000GenomesEuropeSub1006C=0.999A=0.001
1000GenomesGlobalStudy-wide5008C=0.953A=0.047
1000GenomesSouth AsianSub978C=1.000A=0.000
The Genome Aggregation DatabaseAfricanSub8720C=0.862A=0.138
The Genome Aggregation DatabaseAmericanSub838C=0.990A=0.010
The Genome Aggregation DatabaseEast AsianSub1622C=1.000A=0.000
The Genome Aggregation DatabaseEuropeSub18500C=0.999A=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29982C=0.959A=0.040
The Genome Aggregation DatabaseOtherSub302C=1.000A=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.940A=0.059
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
rs170786780.000101alcohol dependence20201924

eQTL of rs17078678 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 rs17078678 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 )
chr132391915623919346E067-38168
chr132391962023919705E067-37809
chr132392254123923011E067-34503
chr132392308523923313E067-34201
chr132393989723940123E067-17391
chr132394047123940581E067-16933
chr132394641623946627E067-10887
chr132394665423947240E067-10274
chr132394730923947554E067-9960
chr132394800323948223E067-9291
chr132394827623948352E067-9162
chr132395516923955224E067-2290
chr132395523923955310E067-2204
chr132395536923955613E067-1901
chr132395570223955776E067-1738
chr132396591523965983E0678401
chr132396598923966175E0678475
chr132396624223966324E0678728
chr132396649123967435E0678977
chr132398109823981317E06723584
chr132398183623981982E06724322
chr132398547023985578E06727956
chr132398583823985935E06728324
chr132398595323986103E06728439
chr132400109524002571E06743581
chr132400505224005092E06747538
chr132400551224005552E06747998
chr132393629223936391E068-21123
chr132394641623946627E068-10887
chr132394665423947240E068-10274
chr132394730923947554E068-9960
chr132394769923947763E068-9751
chr132394784623947913E068-9601
chr132394800323948223E068-9291
chr132394827623948352E068-9162
chr132395146823952746E068-4768
chr132395516923955224E068-2290
chr132395523923955310E068-2204
chr132395536923955613E068-1901
chr132395570223955776E068-1738
chr132395596323956090E068-1424
chr132395613223956311E068-1203
chr132395639223956496E068-1018
chr132395738323957723E0680
chr132395774823957829E068234
chr132395785823957935E068344
chr132395797823958142E068464
chr132396598923966175E0688475
chr132396624223966324E0688728
chr132396649123967435E0688977
chr132396754823967625E06810034
chr132398547023985578E06827956
chr132399913723999177E06841623
chr132399935223999402E06841838
chr132399947523999515E06841961
chr132399952223999580E06842008
chr132400109524002571E06843581
chr132400258524002682E06845071
chr132391915623919346E069-38168
chr132391962023919705E069-37809
chr132394641623946627E069-10887
chr132394665423947240E069-10274
chr132394730923947554E069-9960
chr132395431723954458E069-3056
chr132395477523954975E069-2539
chr132395516923955224E069-2290
chr132395523923955310E069-2204
chr132395536923955613E069-1901
chr132395570223955776E069-1738
chr132395596323956090E069-1424
chr132395613223956311E069-1203
chr132396469523964739E0697181
chr132396591523965983E0698401
chr132396598923966175E0698475
chr132396624223966324E0698728
chr132396649123967435E0698977
chr132396754823967625E06910034
chr132398547023985578E06927956
chr132398583823985935E06928324
chr132398595323986103E06928439
chr132400109524002571E06943581
chr132400551224005552E06947998
chr132391962023919705E070-37809
chr132392254123923011E070-34503
chr132394641623946627E070-10887
chr132394665423947240E070-10274
chr132394730923947554E070-9960
chr132394800323948223E070-9291
chr132395103523951364E070-6150
chr132395146823952746E070-4768
chr132395283623952897E070-4617
chr132395290123953039E070-4475
chr132395309823953211E070-4303
chr132395323523953410E070-4104
chr132395344623953533E070-3981
chr132395353423953632E070-3882
chr132395375523953805E070-3709
chr132395398923954287E070-3227
chr132395431723954458E070-3056
chr132395477523954975E070-2539
chr132395516923955224E070-2290
chr132395523923955310E070-2204
chr132395536923955613E070-1901
chr132395570223955776E070-1738
chr132395596323956090E070-1424
chr132395613223956311E070-1203
chr132395639223956496E070-1018
chr132395738323957723E0700
chr132395774823957829E070234
chr132395785823957935E070344
chr132395797823958142E070464
chr132395818823958280E070674
chr132396624223966324E0708728
chr132396649123967435E0708977
chr132400109524002571E07043581
chr132400258524002682E07045071
chr132400272024002770E07045206
chr132400410824004199E07046594
chr132394665423947240E071-10274
chr132394730923947554E071-9960
chr132395146823952746E071-4768
chr132395398923954287E071-3227
chr132395431723954458E071-3056
chr132395477523954975E071-2539
chr132395516923955224E071-2290
chr132395523923955310E071-2204
chr132395536923955613E071-1901
chr132395570223955776E071-1738
chr132395596323956090E071-1424
chr132395613223956311E071-1203
chr132395639223956496E071-1018
chr132396624223966324E0718728
chr132396649123967435E0718977
chr132400109524002571E07143581
chr132400258524002682E07145071
chr132400551224005552E07147998
chr132400572424005873E07148210
chr132400609524006148E07148581
chr132395146823952746E072-4768
chr132395431723954458E072-3056
chr132395477523954975E072-2539
chr132395516923955224E072-2290
chr132395523923955310E072-2204
chr132395536923955613E072-1901
chr132395570223955776E072-1738
chr132395596323956090E072-1424
chr132396563023965744E0728116
chr132396591523965983E0728401
chr132396598923966175E0728475
chr132396624223966324E0728728
chr132396649123967435E0728977
chr132396754823967625E07210034
chr132396763123967681E07210117
chr132400109524002571E07243581
chr132400505224005092E07247538
chr132391915623919346E073-38168
chr132395146823952746E073-4768
chr132400109524002571E07343581
chr132400551224005552E07347998
chr132391902923919141E074-38373
chr132391962023919705E074-37809
chr132394665423947240E074-10274
chr132394730923947554E074-9960
chr132394769923947763E074-9751
chr132394784623947913E074-9601
chr132394800323948223E074-9291
chr132394827623948352E074-9162
chr132395146823952746E074-4768
chr132395516923955224E074-2290
chr132395523923955310E074-2204
chr132395536923955613E074-1901
chr132395570223955776E074-1738
chr132395596323956090E074-1424
chr132395613223956311E074-1203
chr132395639223956496E074-1018
chr132396563023965744E0748116
chr132396591523965983E0748401
chr132396598923966175E0748475
chr132396624223966324E0748728
chr132396649123967435E0748977
chr132396754823967625E07410034
chr132400109524002571E07443581
chr132400572424005873E07448210
chr132400609524006148E07448581
chr132391859823918810E081-38704
chr132391885323918952E081-38562
chr132391902923919141E081-38373
chr132391915623919346E081-38168
chr132391962023919705E081-37809
chr132394641623946627E081-10887
chr132394665423947240E081-10274
chr132395536923955613E081-1901
chr132395570223955776E081-1738
chr132395596323956090E081-1424
chr132395613223956311E081-1203
chr132395639223956496E081-1018
chr132396337823963460E0815864
chr132398547023985578E08127956
chr132398583823985935E08128324
chr132398595323986103E08128439
chr132400505224005092E08147538
chr132400551224005552E08147998
chr132400572424005873E08148210
chr132391962023919705E082-37809
chr132395146823952746E082-4768
chr132395596323956090E082-1424
chr132395738323957723E0820
chr132395774823957829E082234
chr132398547023985578E08227956










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr132394892623950567E067-6947
chr132400638124006805E06748867
chr132400685924007101E06749345
chr132394870123948918E068-8596
chr132394892623950567E068-6947
chr132400638124006805E06848867
chr132400685924007101E06849345
chr132394870123948918E069-8596
chr132394892623950567E069-6947
chr132400638124006805E06948867
chr132400685924007101E06949345
chr132394870123948918E070-8596
chr132394892623950567E070-6947
chr132400638124006805E07048867
chr132400685924007101E07049345
chr132394892623950567E071-6947
chr132400638124006805E07148867
chr132400685924007101E07149345
chr132394870123948918E072-8596
chr132394892623950567E072-6947
chr132400638124006805E07248867
chr132400685924007101E07249345
chr132394892623950567E073-6947
chr132400638124006805E07348867
chr132400685924007101E07349345
chr132394892623950567E074-6947
chr132400638124006805E07448867
chr132400685924007101E07449345
chr132394870123948918E081-8596
chr132394892623950567E081-6947
chr132400638124006805E08148867
chr132400685924007101E08149345
chr132394870123948918E082-8596
chr132394892623950567E082-6947
chr132400638124006805E08248867
chr132400685924007101E08249345