rs642490

Homo sapiens
A>G
PLEKHB1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0151 (4544/29942,GnomAD)
G=0197 (5757/29118,TOPMED)
G=0164 (819/5008,1000G)
G=0056 (214/3854,ALSPAC)
G=0053 (198/3708,TWINSUK)
chr11:73654570 (GRCh38.p7) (11q13.4)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.73654570A>G
GRCh37.p13 chr 11NC_000011.9:g.73365615A>G

Gene: PLEKHB1, pleckstrin homology domain containing B1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PLEKHB1 transcript variant 3NM_001130033.1:c.N/AIntron Variant
PLEKHB1 transcript variant 2NM_001130034.1:c.N/AIntron Variant
PLEKHB1 transcript variant 4NM_001130035.1:c.N/AIntron Variant
PLEKHB1 transcript variant 5NM_001130036.1:c.N/AIntron Variant
PLEKHB1 transcript variant 1NM_021200.2:c.N/AIntron Variant
PLEKHB1 transcript variant X1XM_011545192.2:c.N/AIntron Variant
PLEKHB1 transcript variant X2XM_011545193.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.570G=0.430
1000GenomesAmericanSub694A=0.910G=0.090
1000GenomesEast AsianSub1008A=0.975G=0.025
1000GenomesEuropeSub1006A=0.929G=0.071
1000GenomesGlobalStudy-wide5008A=0.836G=0.164
1000GenomesSouth AsianSub978A=0.900G=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.944G=0.056
The Genome Aggregation DatabaseAfricanSub8694A=0.625G=0.375
The Genome Aggregation DatabaseAmericanSub838A=0.950G=0.050
The Genome Aggregation DatabaseEast AsianSub1620A=0.994G=0.006
The Genome Aggregation DatabaseEuropeSub18488A=0.935G=0.064
The Genome Aggregation DatabaseGlobalStudy-wide29942A=0.848G=0.151
The Genome Aggregation DatabaseOtherSub302A=0.870G=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.802G=0.197
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.947G=0.053
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
rs6424900.000628alcohol dependence21314694

eQTL of rs642490 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 rs642490 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 )
chr117336142773361500E067-4115
chr117336161673361682E067-3933
chr117336178473361855E067-3760
chr117336243973362537E067-3078
chr117336271173362765E067-2850
chr117336283973363910E067-1705
chr117336399473364249E067-1366
chr117336433173364518E067-1097
chr117336455273364709E067-906
chr117336479173364880E067-735
chr117336513673365340E067-275
chr117336537473365469E067-146
chr117336553173365581E067-34
chr117336559173365654E0670
chr117336583173365881E067216
chr117336593973365979E067324
chr117337107873371376E0675463
chr117337149073371550E0675875
chr117337432673374408E0678711
chr117337445773374507E0678842
chr117337457773374671E0678962
chr117337482773374907E0679212
chr117337494173375231E0679326
chr117337527673375349E0679661
chr117334416173344311E068-21304
chr117334440373344453E068-21162
chr117334446773344535E068-21080
chr117334513273345529E068-20086
chr117335784973357938E068-7677
chr117335795073358206E068-7409
chr117336060273360681E068-4934
chr117336142773361500E068-4115
chr117336161673361682E068-3933
chr117336178473361855E068-3760
chr117336243973362537E068-3078
chr117336271173362765E068-2850
chr117336399473364249E068-1366
chr117336433173364518E068-1097
chr117336455273364709E068-906
chr117336479173364880E068-735
chr117336513673365340E068-275
chr117336537473365469E068-146
chr117336553173365581E068-34
chr117336559173365654E0680
chr117337107873371376E0685463
chr117337149073371550E0685875
chr117337390473374090E0688289
chr117337412973374205E0688514
chr117337432673374408E0688711
chr117337445773374507E0688842
chr117337457773374671E0688962
chr117337482773374907E0689212
chr117337494173375231E0689326
chr117337527673375349E0689661
chr117337542173375533E0689806
chr117337566073375759E06810045
chr117337587173375921E06810256
chr117337598673376159E06810371
chr117334416173344311E069-21304
chr117334440373344453E069-21162
chr117334446773344535E069-21080
chr117335795073358206E069-7409
chr117336047273360560E069-5055
chr117336060273360681E069-4934
chr117336081973360873E069-4742
chr117336102073361134E069-4481
chr117336142773361500E069-4115
chr117336161673361682E069-3933
chr117336178473361855E069-3760
chr117336243973362537E069-3078
chr117336271173362765E069-2850
chr117336399473364249E069-1366
chr117336433173364518E069-1097
chr117336455273364709E069-906
chr117336479173364880E069-735
chr117336513673365340E069-275
chr117336537473365469E069-146
chr117336553173365581E069-34
chr117336559173365654E0690
chr117337086273370933E0695247
chr117337094373370983E0695328
chr117337149073371550E0695875
chr117337412973374205E0698514
chr117337432673374408E0698711
chr117337445773374507E0698842
chr117337457773374671E0698962
chr117337482773374907E0699212
chr117337494173375231E0699326
chr117337527673375349E0699661
chr117337542173375533E0699806
chr117337566073375759E06910045
chr117337587173375921E06910256
chr117337598673376159E06910371
chr117336283973363910E070-1705
chr117333626273336405E071-29210
chr117333679073337175E071-28440
chr117334416173344311E071-21304
chr117334440373344453E071-21162
chr117334446773344535E071-21080
chr117334471173344829E071-20786
chr117336047273360560E071-5055
chr117336060273360681E071-4934
chr117336081973360873E071-4742
chr117336102073361134E071-4481
chr117336142773361500E071-4115
chr117336161673361682E071-3933
chr117336178473361855E071-3760
chr117336243973362537E071-3078
chr117336271173362765E071-2850
chr117336399473364249E071-1366
chr117336433173364518E071-1097
chr117336455273364709E071-906
chr117336479173364880E071-735
chr117336513673365340E071-275
chr117336537473365469E071-146
chr117336553173365581E071-34
chr117336559173365654E0710
chr117336583173365881E071216
chr117336593973365979E071324
chr117336638373366439E071768
chr117337038973370490E0714774
chr117337055373370711E0714938
chr117337077073370855E0715155
chr117337086273370933E0715247
chr117337094373370983E0715328
chr117337107873371376E0715463
chr117337149073371550E0715875
chr117337432673374408E0718711
chr117337445773374507E0718842
chr117337457773374671E0718962
chr117337482773374907E0719212
chr117337494173375231E0719326
chr117339698073397163E07131365
chr117333679073337175E072-28440
chr117333740973337459E072-28156
chr117334416173344311E072-21304
chr117334440373344453E072-21162
chr117334446773344535E072-21080
chr117334471173344829E072-20786
chr117335795073358206E072-7409
chr117336060273360681E072-4934
chr117336081973360873E072-4742
chr117336102073361134E072-4481
chr117336142773361500E072-4115
chr117336161673361682E072-3933
chr117336178473361855E072-3760
chr117336243973362537E072-3078
chr117336271173362765E072-2850
chr117336399473364249E072-1366
chr117336433173364518E072-1097
chr117336455273364709E072-906
chr117336479173364880E072-735
chr117336513673365340E072-275
chr117336537473365469E072-146
chr117336553173365581E072-34
chr117336559173365654E0720
chr117337107873371376E0725463
chr117337149073371550E0725875
chr117337457773374671E0728962
chr117337482773374907E0729212
chr117337494173375231E0729326
chr117337527673375349E0729661
chr117337542173375533E0729806
chr117337566073375759E07210045
chr117335784973357938E073-7677
chr117335795073358206E073-7409
chr117336018273360271E073-5344
chr117336047273360560E073-5055
chr117336060273360681E073-4934
chr117336081973360873E073-4742
chr117336102073361134E073-4481
chr117336142773361500E073-4115
chr117336161673361682E073-3933
chr117336178473361855E073-3760
chr117336243973362537E073-3078
chr117336271173362765E073-2850
chr117336283973363910E073-1705
chr117336399473364249E073-1366
chr117336433173364518E073-1097
chr117336455273364709E073-906
chr117336479173364880E073-735
chr117336513673365340E073-275
chr117336537473365469E073-146
chr117336553173365581E073-34
chr117336559173365654E0730
chr117336583173365881E073216
chr117336593973365979E073324
chr117337149073371550E0735875
chr117337457773374671E0738962
chr117337482773374907E0739212
chr117337494173375231E0739326
chr117337527673375349E0739661
chr117337542173375533E0739806
chr117337566073375759E07310045
chr117333679073337175E074-28440
chr117334416173344311E074-21304
chr117334440373344453E074-21162
chr117334446773344535E074-21080
chr117334471173344829E074-20786
chr117335795073358206E074-7409
chr117336081973360873E074-4742
chr117336102073361134E074-4481
chr117336142773361500E074-4115
chr117336161673361682E074-3933
chr117336178473361855E074-3760
chr117336243973362537E074-3078
chr117336271173362765E074-2850
chr117336399473364249E074-1366
chr117336433173364518E074-1097
chr117336455273364709E074-906
chr117336479173364880E074-735
chr117336513673365340E074-275
chr117336537473365469E074-146
chr117336553173365581E074-34
chr117336559173365654E0740
chr117336583173365881E074216
chr117336593973365979E074324
chr117336638373366439E074768
chr117337038973370490E0744774
chr117337055373370711E0744938
chr117337077073370855E0745155
chr117337086273370933E0745247
chr117337094373370983E0745328
chr117337107873371376E0745463
chr117337149073371550E0745875
chr117337494173375231E0749326
chr117337527673375349E0749661
chr117337542173375533E0749806
chr117337566073375759E07410045
chr117337587173375921E07410256
chr117337598673376159E07410371
chr117335795073358206E081-7409