rs2317457

Homo sapiens
G>A
RAP1GAP2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0206 (6153/29866,GnomAD)
A=0167 (4871/29118,TOPMED)
A=0242 (1214/5008,1000G)
A=0207 (799/3854,ALSPAC)
A=0192 (711/3708,TWINSUK)
chr17:2849919 (GRCh38.p7) (17p13.3)
ND
GWASdb2
1   publication(s)
See rs on genome
54 Enhancers around
5 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.2849919G>A
GRCh37.p13 chr 17NC_000017.10:g.2753213G>A
RAP1GAP2 RefSeqGeneNG_013030.1:g.58482G>A

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 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 X3XM_005256542.2:c.N/AGenic Upstream Transcript 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=0.858A=0.142
1000GenomesAmericanSub694G=0.720A=0.280
1000GenomesEast AsianSub1008G=0.689A=0.311
1000GenomesEuropeSub1006G=0.805A=0.195
1000GenomesGlobalStudy-wide5008G=0.758A=0.242
1000GenomesSouth AsianSub978G=0.670A=0.330
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.793A=0.207
The Genome Aggregation DatabaseAfricanSub8696G=0.865A=0.135
The Genome Aggregation DatabaseAmericanSub836G=0.710A=0.290
The Genome Aggregation DatabaseEast AsianSub1610G=0.694A=0.306
The Genome Aggregation DatabaseEuropeSub18422G=0.772A=0.228
The Genome Aggregation DatabaseGlobalStudy-wide29866G=0.794A=0.206
The Genome Aggregation DatabaseOtherSub302G=0.860A=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.832A=0.167
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.808A=0.192
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs23174570.000898nicotine smoking19268276

eQTL of rs2317457 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 rs2317457 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 )
chr1727119572711997E067-41216
chr1727254802725559E067-27654
chr1727280582728879E067-24334
chr1727316662732239E067-20974
chr1727152752715842E068-37371
chr1727158752715977E068-37236
chr1727190882719622E068-33591
chr1727280582728879E069-24334
chr1727289232729205E069-24008
chr1727773482778112E07024135
chr1727781312778222E07024918
chr1727051002705532E071-47681
chr1727033872703437E072-49776
chr1727122702712310E072-40903
chr1727123312712422E072-40791
chr1727124962712557E072-40656
chr1727125822712751E072-40462
chr1727280582728879E072-24334
chr1727113792711491E073-41722
chr1727119572711997E073-41216
chr1727518922751977E073-1236
chr1727520362752550E073-663
chr1727860872786164E07332874
chr1727864262786500E07333213
chr1727866382786738E07333425
chr1727869082787513E07333695
chr1727033872703437E081-49776
chr1727048242705035E081-48178
chr1727051002705532E081-47681
chr1727058722705922E081-47291
chr1727499982750048E081-3165
chr1727500592750109E081-3104
chr1727501272750177E081-3036
chr1727502072750295E081-2918
chr1727506592751718E081-1495
chr1727518922751977E081-1236
chr1727520362752550E081-663
chr1727653722765549E08112159
chr1727656572765761E08112444
chr1727659292766048E08112716
chr1727663492766491E08113136
chr1728009142801177E08147701
chr1728013972801462E08148184
chr1728014772801780E08148264
chr1728017962801973E08148583
chr1728019992802198E08148786
chr1728023392802389E08149126
chr1727051002705532E082-47681
chr1727500592750109E082-3104
chr1727501272750177E082-3036
chr1727653722765549E08212159
chr1727656572765761E08212444
chr1727659292766048E08212716
chr1727866382786738E08233425









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1727551982758795E0671985
chr1727551982758795E0691985
chr1727551982758795E0711985
chr1727551982758795E0731985
chr1727551982758795E0821985