rs17835089

Homo sapiens
G>C
RAP1GAP2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0049 (1476/29986,GnomAD)
C=0030 (876/29118,TOPMED)
C=0051 (254/5008,1000G)
C=0059 (228/3854,ALSPAC)
C=0054 (200/3708,TWINSUK)
chr17:2907378 (GRCh38.p7) (17p13.3)
AD
GWASdb2
1   publication(s)
See rs on genome
115 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.2907378G>C
GRCh37.p13 chr 17NC_000017.10:g.2810672G>C
RAP1GAP2 RefSeqGeneNG_013030.1:g.115941G>C

Gene: RAP1GAP2, RAP1 GTPase activating protein 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
RAP1GAP2 transcript variant 2NM_001100398.1:c.N/AIntron Variant
RAP1GAP2 transcript variant 1NM_015085.4:c.N/AIntron Variant
RAP1GAP2 transcript variant X3XM_005256542.2:c.N/AIntron Variant
RAP1GAP2 transcript variant X5XM_006721477.3:c.N/AIntron Variant
RAP1GAP2 transcript variant X1XM_011523738.1:c.N/AIntron Variant
RAP1GAP2 transcript variant X2XM_011523739.1:c.N/AIntron Variant
RAP1GAP2 transcript variant X4XM_011523740.2:c.N/AIntron Variant
RAP1GAP2 transcript variant X4XM_011523741.2:c.N/AIntron Variant
RAP1GAP2 transcript variant X7XM_017024370.1:c.N/AIntron Variant
RAP1GAP2 transcript variant X5XM_017024371.1:c.N/AIntron Variant
RAP1GAP2 transcript variant X6XM_011523742.2:c.N/AGenic Upstream Transcript Variant
RAP1GAP2 transcript variant X7XM_011523743.2:c.N/AGenic Upstream Transcript Variant
RAP1GAP2 transcript variant X8XM_011523744.2:c.N/AGenic Upstream Transcript Variant
RAP1GAP2 transcript variant X10XM_011523745.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.997C=0.003
1000GenomesAmericanSub694G=0.970C=0.030
1000GenomesEast AsianSub1008G=0.961C=0.039
1000GenomesEuropeSub1006G=0.933C=0.067
1000GenomesGlobalStudy-wide5008G=0.949C=0.051
1000GenomesSouth AsianSub978G=0.880C=0.120
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.941C=0.059
The Genome Aggregation DatabaseAfricanSub8734G=0.993C=0.007
The Genome Aggregation DatabaseAmericanSub838G=0.980C=0.020
The Genome Aggregation DatabaseEast AsianSub1622G=0.953C=0.047
The Genome Aggregation DatabaseEuropeSub18490G=0.929C=0.070
The Genome Aggregation DatabaseGlobalStudy-wide29986G=0.950C=0.049
The Genome Aggregation DatabaseOtherSub302G=0.940C=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.969C=0.030
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.946C=0.054
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
rs178350890.000498alcohol dependence21314694

eQTL of rs17835089 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr17:2810672HNRNPA1P16ENSG00000262333.1G>C8.7038e-3600617Brain_Spinal_cord_cervical

meQTL of rs17835089 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 )
chr1728064772806907E067-3765
chr1728069962807046E067-3626
chr1728070772808066E067-2606
chr1728081102808160E067-2512
chr1728125662812738E0671894
chr1728070772808066E068-2606
chr1728405442840708E06829872
chr1728407542841196E06830082
chr1728412092841271E06830537
chr1728429892843355E06832317
chr1728433872843508E06832715
chr1728435252844005E06832853
chr1728441372844217E06833465
chr1728061342806474E069-4198
chr1728064772806907E069-3765
chr1728069962807046E069-3626
chr1728070772808066E069-2606
chr1728081102808160E069-2512
chr1728272792827329E06916607
chr1728404582840498E06929786
chr1728405442840708E06929872
chr1728412092841271E06930537
chr1728441372844217E06933465
chr1728443282844378E06933656
chr1727773482778112E070-32560
chr1727781312778222E070-32450
chr1728060392806079E070-4593
chr1728061342806474E070-4198
chr1728064772806907E070-3765
chr1728069962807046E070-3626
chr1728070772808066E070-2606
chr1728069962807046E071-3626
chr1728070772808066E071-2606
chr1728412092841271E07130537
chr1728429892843355E07132317
chr1728433872843508E07132715
chr1728435252844005E07132853
chr1728441372844217E07133465
chr1728454742845536E07134802
chr1728061342806474E072-4198
chr1728064772806907E072-3765
chr1728069962807046E072-3626
chr1728070772808066E072-2606
chr1728081102808160E072-2512
chr1728404582840498E07229786
chr1728405442840708E07229872
chr1728407542841196E07230082
chr1728412092841271E07230537
chr1728414112841461E07230739
chr1728416092841693E07230937
chr1728441372844217E07233465
chr1728443282844378E07233656
chr1727860872786164E073-24508
chr1727864262786500E073-24172
chr1727866382786738E073-23934
chr1727869082787513E073-23159
chr1728064772806907E073-3765
chr1728069962807046E073-3626
chr1728070772808066E073-2606
chr1728081102808160E073-2512
chr1728407542841196E07330082
chr1728412092841271E07330537
chr1727653722765549E081-45123
chr1727656572765761E081-44911
chr1727659292766048E081-44624
chr1727663492766491E081-44181
chr1728009142801177E081-9495
chr1728013972801462E081-9210
chr1728014772801780E081-8892
chr1728017962801973E081-8699
chr1728019992802198E081-8474
chr1728023392802389E081-8283
chr1728032142803649E081-7023
chr1728059382806011E081-4661
chr1728060392806079E081-4593
chr1728061342806474E081-4198
chr1728064772806907E081-3765
chr1728069962807046E081-3626
chr1728070772808066E081-2606
chr1728081102808160E081-2512
chr1728140672814148E0813395
chr1728142512814549E0813579
chr1728146102814685E0813938
chr1728148052814943E0814133
chr1728151132815257E0814441
chr1728153422815430E0814670
chr1728433872843508E08132715
chr1728435252844005E08132853
chr1728494252849826E08138753
chr1728498732850045E08139201
chr1728504242850495E08139752
chr1728505992850681E08139927
chr1728508992850974E08140227
chr1728512032851304E08140531
chr1728513162851424E08140644
chr1728514312851485E08140759
chr1728515222851562E08140850
chr1728515692851685E08140897
chr1728518942851944E08141222
chr1728521612852224E08141489
chr1727653722765549E082-45123
chr1727656572765761E082-44911
chr1727659292766048E082-44624
chr1727866382786738E082-23934
chr1728061342806474E082-4198
chr1728064772806907E082-3765
chr1728069962807046E082-3626
chr1728081102808160E082-2512
chr1728151132815257E0824441
chr1728153422815430E0824670
chr1728512032851304E08240531
chr1728513162851424E08240644
chr1728514312851485E08240759
chr1728515222851562E08240850
chr1728515692851685E08240897