rs925368

Homo sapiens
T>C
GIT2 : Missense Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0005 (652/121396,ExAC)
C=0004 (126/30000,GnomAD)
C=0000 (4/29118,TOPMED)
T==0000 (1/13006,GO-ESP)
C=0015 (73/5008,1000G)
C=0001 (3/3854,ALSPAC)
C=0000 (0/3708,TWINSUK)
chr12:109953174 (GRCh38.p7) (12q24.11)
AD
GWASdb2
2   publication(s)
See rs on genome
124 Enhancers around
28 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.109953174T>C
GRCh37.p13 chr 12NC_000012.11:g.110390979T>C
GIT2 RefSeqGeneNG_029885.1:g.48216A>G

Gene: GIT2, G protein-coupled receptor kinase interacting ArfGAP 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
GIT2 transcript variant 4NM_139201.2:c.116...NM_139201.2:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform 4NP_631940.2:p.Asn...NP_631940.2:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant 2NM_057170.3:c.116...NM_057170.3:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform 2NP_476511.1:p.Asn...NP_476511.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant 1NM_057169.3:c.116...NM_057169.3:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform 1NP_476510.1:p.Asn...NP_476510.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant 3NM_014776.3:c.116...NM_014776.3:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform 3NP_055591.2:p.Asn...NP_055591.2:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant 6NM_001135213.1:c....NM_001135213.1:c.1166A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform 6NP_001128685.1:p....NP_001128685.1:p.Asn389SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant 5NM_001135214.1:c....NM_001135214.1:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform 5NP_001128686.1:p....NP_001128686.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X1XM_005253997.3:c....XM_005253997.3:c.1157A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X1XP_005254054.1:p....XP_005254054.1:p.Asn386SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X2XM_006719707.3:c....XM_006719707.3:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X2XP_006719770.1:p....XP_006719770.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X3XM_006719708.3:c....XM_006719708.3:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X3XP_006719771.1:p....XP_006719771.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X4XM_017020258.1:c....XM_017020258.1:c.1157A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X4XP_016875747.1:p....XP_016875747.1:p.Asn386SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X5XM_006719709.3:c....XM_006719709.3:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X5XP_006719772.1:p....XP_006719772.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X6XM_005254000.3:c....XM_005254000.3:c.1157A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X6XP_005254057.1:p....XP_005254057.1:p.Asn386SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X7XM_017020259.1:c....XM_017020259.1:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X6XP_016875748.1:p....XP_016875748.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X8XM_017020260.1:c....XM_017020260.1:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X7XP_016875749.1:p....XP_016875749.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X9XM_006719712.3:c....XM_006719712.3:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X8XP_006719775.1:p....XP_006719775.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X10XM_017020261.1:c....XM_017020261.1:c.1157A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X9XP_016875750.1:p....XP_016875750.1:p.Asn386SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X11XM_006719713.3:c....XM_006719713.3:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X10XP_006719776.1:p....XP_006719776.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant
GIT2 transcript variant X12XM_006719714.3:c....XM_006719714.3:c.1160A>GN [AAC]> S [AGC]Coding Sequence Variant
ARF GTPase-activating protein GIT2 isoform X12XP_006719777.1:p....XP_006719777.1:p.Asn387SerN [Asn]> S [Ser]Missense Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=1.000C=0.000
1000GenomesAmericanSub694T=1.000C=0.000
1000GenomesEast AsianSub1008T=0.928C=0.072
1000GenomesEuropeSub1006T=1.000C=0.000
1000GenomesGlobalStudy-wide5008T=0.985C=0.015
1000GenomesSouth AsianSub978T=1.000C=0.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.999C=0.001
The Exome Aggregation ConsortiumAmericanSub21982T=0.999C=0.000
The Exome Aggregation ConsortiumAsianSub25160T=0.974C=0.025
The Exome Aggregation ConsortiumEuropeSub73348T=1.000C=0.000
The Exome Aggregation ConsortiumGlobalStudy-wide121396T=0.994C=0.005
The Exome Aggregation ConsortiumOtherSub906T=1.000C=0.000
The Genome Aggregation DatabaseAfricanSub8732T=1.000C=0.000
The Genome Aggregation DatabaseAmericanSub838T=1.000C=0.000
The Genome Aggregation DatabaseEast AsianSub1622T=0.923C=0.077
The Genome Aggregation DatabaseEuropeSub18506T=0.999C=0.000
The Genome Aggregation DatabaseGlobalStudy-wide30000T=0.995C=0.004
The Genome Aggregation DatabaseOtherSub302T=1.000C=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.999C=0.000
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=1.000C=0.000
PMID Title Author Journal
23555315Genome-wide testing of putative functional exonic variants in relationship with breast and prostate cancer risk in a multiethnic population.Haiman CAPLoS Genet
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs9253681.30E-26alcohol (ever vs. never)23555315
rs9253685.31E-08alcohol consumption (maxi-drinks)24277619

eQTL of rs925368 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 rs925368 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 )
chr12110370723110371221E067-19758
chr12110374725110375215E067-15764
chr12110375247110375509E067-15470
chr12110384359110384740E067-6239
chr12110384816110384898E067-6081
chr12110384984110385156E067-5823
chr12110385205110385361E067-5618
chr12110385394110385909E067-5070
chr12110386003110386065E067-4914
chr12110386088110387359E067-3620
chr12110426772110426926E06735793
chr12110426927110427008E06735948
chr12110427094110427174E06736115
chr12110431333110431402E06740354
chr12110367523110367794E068-23185
chr12110374725110375215E068-15764
chr12110375247110375509E068-15470
chr12110382717110383304E068-7675
chr12110384359110384740E068-6239
chr12110384816110384898E068-6081
chr12110384984110385156E068-5823
chr12110385205110385361E068-5618
chr12110385394110385909E068-5070
chr12110386003110386065E068-4914
chr12110386088110387359E068-3620
chr12110390249110390569E068-410
chr12110390638110390711E068-268
chr12110426772110426926E06835793
chr12110426927110427008E06835948
chr12110427094110427174E06836115
chr12110427243110427602E06836264
chr12110428226110428276E06837247
chr12110429610110429660E06838631
chr12110431786110431865E06840807
chr12110439281110439346E06848302
chr12110439383110440172E06848404
chr12110440234110440300E06849255
chr12110370723110371221E069-19758
chr12110374725110375215E069-15764
chr12110375247110375509E069-15470
chr12110382717110383304E069-7675
chr12110384359110384740E069-6239
chr12110384816110384898E069-6081
chr12110384984110385156E069-5823
chr12110385205110385361E069-5618
chr12110385394110385909E069-5070
chr12110386003110386065E069-4914
chr12110386088110387359E069-3620
chr12110426927110427008E06935948
chr12110427094110427174E06936115
chr12110427243110427602E06936264
chr12110431699110431771E06940720
chr12110431786110431865E06940807
chr12110438876110438924E06947897
chr12110438985110439085E06948006
chr12110439102110439169E06948123
chr12110370259110370691E071-20288
chr12110370723110371221E071-19758
chr12110374725110375215E071-15764
chr12110375247110375509E071-15470
chr12110384359110384740E071-6239
chr12110384816110384898E071-6081
chr12110384984110385156E071-5823
chr12110385205110385361E071-5618
chr12110385394110385909E071-5070
chr12110386003110386065E071-4914
chr12110386088110387359E071-3620
chr12110426772110426926E07135793
chr12110426927110427008E07135948
chr12110427094110427174E07136115
chr12110427243110427602E07136264
chr12110438985110439085E07148006
chr12110439102110439169E07148123
chr12110370723110371221E072-19758
chr12110374725110375215E072-15764
chr12110375247110375509E072-15470
chr12110384359110384740E072-6239
chr12110384816110384898E072-6081
chr12110384984110385156E072-5823
chr12110385205110385361E072-5618
chr12110385394110385909E072-5070
chr12110386003110386065E072-4914
chr12110386088110387359E072-3620
chr12110426772110426926E07235793
chr12110426927110427008E07235948
chr12110427094110427174E07236115
chr12110427243110427602E07236264
chr12110428226110428276E07237247
chr12110428537110428589E07237558
chr12110435072110435166E07244093
chr12110435180110435380E07244201
chr12110374725110375215E073-15764
chr12110375247110375509E073-15470
chr12110384359110384740E073-6239
chr12110384816110384898E073-6081
chr12110384984110385156E073-5823
chr12110385205110385361E073-5618
chr12110385394110385909E073-5070
chr12110386003110386065E073-4914
chr12110386088110387359E073-3620
chr12110426772110426926E07335793
chr12110426927110427008E07335948
chr12110440234110440300E07349255
chr12110369903110369953E074-21026
chr12110370259110370691E074-20288
chr12110370723110371221E074-19758
chr12110374725110375215E074-15764
chr12110375247110375509E074-15470
chr12110382717110383304E074-7675
chr12110384359110384740E074-6239
chr12110384816110384898E074-6081
chr12110384984110385156E074-5823
chr12110385205110385361E074-5618
chr12110385394110385909E074-5070
chr12110386003110386065E074-4914
chr12110386088110387359E074-3620
chr12110426772110426926E07435793
chr12110426927110427008E07435948
chr12110427094110427174E07436115
chr12110427243110427602E07436264
chr12110428226110428276E07437247
chr12110431786110431865E07440807
chr12110438876110438924E07447897
chr12110438985110439085E07448006







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr12110433229110434638E06742250
chr12110435995110437624E06745016
chr12110437640110438282E06746661
chr12110433229110434638E06842250
chr12110435995110437624E06845016
chr12110437640110438282E06846661
chr12110433229110434638E06942250
chr12110435995110437624E06945016
chr12110437640110438282E06946661
chr12110433229110434638E07042250
chr12110435995110437624E07045016
chr12110437640110438282E07046661
chr12110433229110434638E07142250
chr12110435995110437624E07145016
chr12110437640110438282E07146661
chr12110433229110434638E07242250
chr12110435995110437624E07245016
chr12110437640110438282E07246661
chr12110433229110434638E07342250
chr12110435995110437624E07345016
chr12110437640110438282E07346661
chr12110433229110434638E07442250
chr12110435995110437624E07445016
chr12110437640110438282E07446661
chr12110435995110437624E08145016
chr12110437640110438282E08146661
chr12110433229110434638E08242250
chr12110435995110437624E08245016