rs17198978

Homo sapiens
C>T
PTPRJ : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0074 (2232/29964,GnomAD)
T=0069 (2033/29118,TOPMED)
T=0112 (561/5008,1000G)
T=0085 (329/3854,ALSPAC)
T=0088 (325/3708,TWINSUK)
chr11:48150813 (GRCh38.p7) (11p11.2)
ND
GWASdb2
2   publication(s)
See rs on genome
225 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.48150813C>T
GRCh37.p13 chr 11NC_000011.9:g.48172365C>T
PTPRJ RefSeqGeneNG_012209.1:g.175256C>T

Gene: PTPRJ, protein tyrosine phosphatase, receptor type J(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PTPRJ transcript variant 1NM_002843.3:c.N/AIntron Variant
PTPRJ transcript variant 2NM_001098503.1:c.N/AGenic Downstream Transcript Variant
PTPRJ transcript variant X1XM_017018083.1:c.N/AIntron Variant
PTPRJ transcript variant X2XM_017018084.1:c.N/AIntron Variant
PTPRJ transcript variant X3XM_017018085.1:c.N/AIntron Variant
PTPRJ transcript variant X4XR_930883.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.996T=0.004
1000GenomesAmericanSub694C=0.920T=0.080
1000GenomesEast AsianSub1008C=0.769T=0.231
1000GenomesEuropeSub1006C=0.909T=0.091
1000GenomesGlobalStudy-wide5008C=0.888T=0.112
1000GenomesSouth AsianSub978C=0.820T=0.180
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.915T=0.085
The Genome Aggregation DatabaseAfricanSub8724C=0.980T=0.020
The Genome Aggregation DatabaseAmericanSub838C=0.930T=0.070
The Genome Aggregation DatabaseEast AsianSub1614C=0.797T=0.203
The Genome Aggregation DatabaseEuropeSub18488C=0.912T=0.087
The Genome Aggregation DatabaseGlobalStudy-wide29964C=0.925T=0.074
The Genome Aggregation DatabaseOtherSub300C=0.850T=0.150
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.930T=0.069
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.912T=0.088
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs171989780.00000546alcohol and nictotine co-dependence20158304
rs171989780.000233nicotine smoking19268276

eQTL of rs17198978 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 rs17198978 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 )
chr114812271548122802E067-49563
chr114812297448123237E067-49128
chr114812329448123940E067-48425
chr114812434248124406E067-47959
chr114812451248124595E067-47770
chr114812508548126264E067-46101
chr114812627648126488E067-45877
chr114812667748126953E067-45412
chr114812699348127055E067-45310
chr114812705648127134E067-45231
chr114812718548127344E067-45021
chr114812776348128168E067-44197
chr114812871448129343E067-43022
chr114813027048130610E067-41755
chr114813061948131808E067-40557
chr114814548648145536E067-26829
chr114814571248146145E067-26220
chr114814618548146271E067-26094
chr114814635848146525E067-25840
chr114814680148146934E067-25431
chr114814698848147028E067-25337
chr114818364948183809E06711284
chr114818389548184254E06711530
chr114818438348184433E06712018
chr114818452648184698E06712161
chr114818471148184968E06712346
chr114818643548186772E06714070
chr114818700348187379E06714638
chr114819046848190633E06718103
chr114819068248190992E06718317
chr114819104648191135E06718681
chr114819120948192854E06718844
chr114812271548122802E068-49563
chr114812297448123237E068-49128
chr114812434248124406E068-47959
chr114812451248124595E068-47770
chr114812627648126488E068-45877
chr114812667748126953E068-45412
chr114812699348127055E068-45310
chr114812705648127134E068-45231
chr114812718548127344E068-45021
chr114812776348128168E068-44197
chr114812871448129343E068-43022
chr114812961648129660E068-42705
chr114812985448130059E068-42306
chr114813007048130255E068-42110
chr114813027048130610E068-41755
chr114813197348132114E068-40251
chr114814618548146271E068-26094
chr114814635848146525E068-25840
chr114814680148146934E068-25431
chr114814698848147028E068-25337
chr114818351148183564E06811146
chr114818364948183809E06811284
chr114818389548184254E06811530
chr114818438348184433E06812018
chr114818452648184698E06812161
chr114818471148184968E06812346
chr114818506348185113E06812698
chr114819104648191135E06818681
chr114819120948192854E06818844
chr114812271548122802E069-49563
chr114812297448123237E069-49128
chr114812329448123940E069-48425
chr114812434248124406E069-47959
chr114812451248124595E069-47770
chr114812508548126264E069-46101
chr114812627648126488E069-45877
chr114812667748126953E069-45412
chr114812699348127055E069-45310
chr114812705648127134E069-45231
chr114812718548127344E069-45021
chr114812871448129343E069-43022
chr114812961648129660E069-42705
chr114812985448130059E069-42306
chr114813007048130255E069-42110
chr114813027048130610E069-41755
chr114813061948131808E069-40557
chr114814571248146145E069-26220
chr114814618548146271E069-26094
chr114814635848146525E069-25840
chr114814680148146934E069-25431
chr114814698848147028E069-25337
chr114816310148163339E069-9026
chr114816336748163519E069-8846
chr114818364948183809E06911284
chr114818389548184254E06911530
chr114818438348184433E06912018
chr114818452648184698E06912161
chr114818471148184968E06912346
chr114818506348185113E06912698
chr114818512748185795E06912762
chr114819104648191135E06918681
chr114819120948192854E06918844
chr114813027048130610E070-41755
chr114812271548122802E071-49563
chr114812297448123237E071-49128
chr114812329448123940E071-48425
chr114812434248124406E071-47959
chr114812451248124595E071-47770
chr114812627648126488E071-45877
chr114812667748126953E071-45412
chr114812699348127055E071-45310
chr114812705648127134E071-45231
chr114812718548127344E071-45021
chr114812776348128168E071-44197
chr114812871448129343E071-43022
chr114812961648129660E071-42705
chr114812985448130059E071-42306
chr114813007048130255E071-42110
chr114813027048130610E071-41755
chr114813061948131808E071-40557
chr114814571248146145E071-26220
chr114814618548146271E071-26094
chr114814635848146525E071-25840
chr114814680148146934E071-25431
chr114814698848147028E071-25337
chr114816310148163339E071-9026
chr114816336748163519E071-8846
chr114818389548184254E07111530
chr114818438348184433E07112018
chr114818452648184698E07112161
chr114818471148184968E07112346
chr114818506348185113E07112698
chr114818643548186772E07114070
chr114819104648191135E07118681
chr114819120948192854E07118844
chr114819317848193366E07120813
chr114812271548122802E072-49563
chr114812434248124406E072-47959
chr114812451248124595E072-47770
chr114812508548126264E072-46101
chr114812627648126488E072-45877
chr114812667748126953E072-45412
chr114812699348127055E072-45310
chr114812705648127134E072-45231
chr114812718548127344E072-45021
chr114812776348128168E072-44197
chr114812871448129343E072-43022
chr114812961648129660E072-42705
chr114812985448130059E072-42306
chr114813007048130255E072-42110
chr114813027048130610E072-41755
chr114813061948131808E072-40557
chr114814571248146145E072-26220
chr114814618548146271E072-26094
chr114814635848146525E072-25840
chr114818351148183564E07211146
chr114818364948183809E07211284
chr114818389548184254E07211530
chr114818438348184433E07212018
chr114818700348187379E07214638
chr114819120948192854E07218844
chr114812271548122802E073-49563
chr114812297448123237E073-49128
chr114812329448123940E073-48425
chr114812434248124406E073-47959
chr114812451248124595E073-47770
chr114812508548126264E073-46101
chr114812627648126488E073-45877
chr114812667748126953E073-45412
chr114812699348127055E073-45310
chr114812705648127134E073-45231
chr114812718548127344E073-45021
chr114812985448130059E073-42306
chr114813007048130255E073-42110
chr114813027048130610E073-41755
chr114813061948131808E073-40557
chr114815838548158811E073-13554
chr114815890748159161E073-13204
chr114818389548184254E07311530
chr114818438348184433E07312018
chr114818452648184698E07312161
chr114819120948192854E07318844
chr114819317848193366E07320813
chr114812271548122802E074-49563
chr114812297448123237E074-49128
chr114812329448123940E074-48425
chr114812434248124406E074-47959
chr114812451248124595E074-47770
chr114812508548126264E074-46101
chr114812627648126488E074-45877
chr114812667748126953E074-45412
chr114812699348127055E074-45310
chr114812705648127134E074-45231
chr114812718548127344E074-45021
chr114812776348128168E074-44197
chr114812871448129343E074-43022
chr114812961648129660E074-42705
chr114812985448130059E074-42306
chr114813007048130255E074-42110
chr114813027048130610E074-41755
chr114813061948131808E074-40557
chr114814618548146271E074-26094
chr114814635848146525E074-25840
chr114814680148146934E074-25431
chr114814698848147028E074-25337
chr114816288848162938E074-9427
chr114816310148163339E074-9026
chr114816336748163519E074-8846
chr114818364948183809E07411284
chr114818389548184254E07411530
chr114818438348184433E07412018
chr114819104648191135E07418681
chr114819120948192854E07418844
chr114812297448123237E081-49128
chr114812329448123940E081-48425
chr114813061948131808E081-40557
chr114813186648131972E081-40393
chr114813197348132114E081-40251
chr114818351148183564E08111146
chr114818364948183809E08111284
chr114818389548184254E08111530
chr114818438348184433E08112018
chr114818452648184698E08112161
chr114818471148184968E08112346
chr114818506348185113E08112698
chr114818512748185795E08112762
chr114818594948186068E08113584
chr114818389548184254E08211530
chr114818438348184433E08212018
chr114818452648184698E08212161
chr114818471148184968E08212346
chr114818506348185113E08212698
chr114818512748185795E08212762