rs6786239

Homo sapiens
C>T
ATP2B2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0114 (3427/29918,GnomAD)
T=0121 (3528/29118,TOPMED)
T=0104 (520/5008,1000G)
T=0142 (549/3854,ALSPAC)
T=0142 (528/3708,TWINSUK)
chr3:10407088 (GRCh38.p7) (3p25.3)
CD
GWASdb2
1   publication(s)
See rs on genome
92 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.10407088C>T
GRCh37.p13 chr 3NC_000003.11:g.10448772C>T
ATP2B2 RefSeqGeneNG_012046.1:g.103497G>A

Gene: ATP2B2, ATPase plasma membrane Ca2+ transporting 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ATP2B2 transcript variant 1NM_001001331.2:c.N/AIntron Variant
ATP2B2 transcript variant 2NM_001683.3:c.N/AIntron Variant
ATP2B2 transcript variant X2XM_005265179.4:c.N/AIntron Variant
ATP2B2 transcript variant X1XM_006713175.3:c.N/AIntron Variant
ATP2B2 transcript variant X4XM_011533752.2:c.N/AIntron Variant
ATP2B2 transcript variant X3XM_017006481.1:c.N/AIntron Variant
ATP2B2 transcript variant X5XM_017006482.1:c.N/AIntron Variant
ATP2B2 transcript variant X6XM_017006483.1:c.N/AIntron Variant
ATP2B2 transcript variant X7XM_017006484.1:c.N/AIntron Variant
ATP2B2 transcript variant X8XM_017006485.1:c.N/AIntron Variant
ATP2B2 transcript variant X9XM_017006486.1:c.N/AIntron Variant
ATP2B2 transcript variant X10XM_017006487.1:c.N/AIntron Variant
ATP2B2 transcript variant X11XM_017006488.1:c.N/AIntron Variant
ATP2B2 transcript variant X12XM_017006489.1:c.N/AIntron Variant
ATP2B2 transcript variant X13XM_017006490.1:c.N/AIntron Variant
ATP2B2 transcript variant X14XM_017006491.1:c.N/AIntron Variant
ATP2B2 transcript variant X15XM_017006492.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.952T=0.048
1000GenomesAmericanSub694C=0.750T=0.250
1000GenomesEast AsianSub1008C=0.995T=0.005
1000GenomesEuropeSub1006C=0.876T=0.124
1000GenomesGlobalStudy-wide5008C=0.896T=0.104
1000GenomesSouth AsianSub978C=0.850T=0.150
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.858T=0.142
The Genome Aggregation DatabaseAfricanSub8710C=0.930T=0.070
The Genome Aggregation DatabaseAmericanSub838C=0.760T=0.240
The Genome Aggregation DatabaseEast AsianSub1622C=0.994T=0.006
The Genome Aggregation DatabaseEuropeSub18446C=0.861T=0.138
The Genome Aggregation DatabaseGlobalStudy-wide29918C=0.885T=0.114
The Genome Aggregation DatabaseOtherSub302C=0.840T=0.160
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.878T=0.121
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.858T=0.142
PMID Title Author Journal
23958962Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.Gelernter JMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs67862390.0000033cocaine dependence23958962
rs67862390.000142cocaine dependence23958962

eQTL of rs6786239 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 rs6786239 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 )
chr31042044010420494E067-28278
chr31042270910422871E067-25901
chr31042305010423389E067-25383
chr31043965310439760E067-9012
chr31044017310440308E067-8464
chr31044034510440395E067-8377
chr31045051810450671E0671746
chr31048736810487466E06738596
chr31048931210489503E06740540
chr31048952110489821E06740749
chr31039898410399051E068-49721
chr31041177610411849E068-36923
chr31041547010415677E068-33095
chr31042305010423389E068-25383
chr31043965310439760E068-9012
chr31044017310440308E068-8464
chr31044034510440395E068-8377
chr31047021110470366E06821439
chr31047053410470621E06821762
chr31048736810487466E06838596
chr31041595310416035E069-32737
chr31041612210416249E069-32523
chr31042270910422871E069-25901
chr31042305010423389E069-25383
chr31044017310440308E069-8464
chr31044034510440395E069-8377
chr31047476610474851E06925994
chr31048931210489503E06940540
chr31048952110489821E06940749
chr31040830910408660E070-40112
chr31041595310416035E070-32737
chr31041612210416249E070-32523
chr31041795910418508E070-30264
chr31041972310419818E070-28954
chr31042044010420494E070-28278
chr31042116010421349E070-27423
chr31042270910422871E070-25901
chr31042305010423389E070-25383
chr31049787810497939E07049106
chr31041547010415677E071-33095
chr31041595310416035E071-32737
chr31041612210416249E071-32523
chr31048001010480174E07131238
chr31048931210489503E07140540
chr31039898410399051E072-49721
chr31039933910399644E072-49128
chr31039978510399916E072-48856
chr31041595310416035E072-32737
chr31041612210416249E072-32523
chr31044017310440308E072-8464
chr31044034510440395E072-8377
chr31047021110470366E07221439
chr31047053410470621E07221762
chr31047376610473886E07224994
chr31047400210474484E07225230
chr31048736810487466E07238596
chr31048952110489821E07240749
chr31049032010490407E07241548
chr31039898410399051E073-49721
chr31039933910399644E073-49128
chr31041177610411849E073-36923
chr31041212510412616E073-36156
chr31042044010420494E073-28278
chr31042270910422871E073-25901
chr31042305010423389E073-25383
chr31043965310439760E073-9012
chr31044017310440308E073-8464
chr31044034510440395E073-8377
chr31046378610463835E07315014
chr31046390610463999E07315134
chr31047021110470366E07321439
chr31047053410470621E07321762
chr31047853010478668E07329758
chr31047890710479408E07330135
chr31047942810479512E07330656
chr31047952510479633E07330753
chr31048625610486464E07337484
chr31048652210486572E07337750
chr31048736810487466E07338596
chr31048931210489503E07340540
chr31048952110489821E07340749
chr31041595310416035E074-32737
chr31041612210416249E074-32523
chr31047053410470621E07421762
chr31041795910418508E081-30264
chr31041972310419818E081-28954
chr31042270910422871E081-25901
chr31042305010423389E081-25383
chr31048652210486572E08137750
chr31047053410470621E08221762
chr31048625610486464E08237484
chr31048652210486572E08237750