rs6443238

Homo sapiens
C>T
SETD5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0081 (2432/29940,GnomAD)
T=0122 (3562/29118,TOPMED)
T=0095 (478/5008,1000G)
T=0001 (5/3854,ALSPAC)
T=0000 (1/3708,TWINSUK)
chr3:9407371 (GRCh38.p7) (3p25.3)
AD
GWASdb2
1   publication(s)
See rs on genome
144 Enhancers around
40 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.9407371C>T
GRCh37.p13 chr 3NC_000003.11:g.9449055C>T
SETD5 RefSeqGeneNG_034132.1:g.14672C>T

Gene: SETD5, SET domain containing 5(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SETD5 transcript variant 1NM_001080517.2:c.N/AIntron Variant
SETD5 transcript variant 2NM_001292043.1:c.N/AIntron Variant
SETD5 transcript variant X13XM_005265301.1:c.N/AIntron Variant
SETD5 transcript variant X17XM_005265303.1:c.N/AIntron Variant
SETD5 transcript variant X2XM_011533920.1:c.N/AIntron Variant
SETD5 transcript variant X3XM_011533921.1:c.N/AIntron Variant
SETD5 transcript variant X4XM_011533922.1:c.N/AIntron Variant
SETD5 transcript variant X8XM_011533927.1:c.N/AIntron Variant
SETD5 transcript variant X10XM_011533928.1:c.N/AIntron Variant
SETD5 transcript variant X15XM_011533930.1:c.N/AIntron Variant
SETD5 transcript variant X23XM_011533932.1:c.N/AIntron Variant
SETD5 transcript variant X1XM_017006767.1:c.N/AIntron Variant
SETD5 transcript variant X6XM_017006769.1:c.N/AIntron Variant
SETD5 transcript variant X7XM_017006770.1:c.N/AIntron Variant
SETD5 transcript variant X9XM_017006771.1:c.N/AIntron Variant
SETD5 transcript variant X11XM_017006772.1:c.N/AIntron Variant
SETD5 transcript variant X12XM_017006773.1:c.N/AIntron Variant
SETD5 transcript variant X14XM_017006774.1:c.N/AIntron Variant
SETD5 transcript variant X16XM_017006775.1:c.N/AIntron Variant
SETD5 transcript variant X19XM_017006776.1:c.N/AIntron Variant
SETD5 transcript variant X20XM_017006777.1:c.N/AIntron Variant
SETD5 transcript variant X21XM_017006778.1:c.N/AIntron Variant
SETD5 transcript variant X22XM_017006779.1:c.N/AIntron Variant
SETD5 transcript variant X24XM_017006780.1:c.N/AIntron Variant
SETD5 transcript variant X25XM_017006781.1:c.N/AIntron Variant
SETD5 transcript variant X26XM_017006782.1:c.N/AIntron Variant
SETD5 transcript variant X27XM_017006783.1:c.N/AIntron Variant
SETD5 transcript variant X28XM_017006784.1:c.N/AIntron Variant
SETD5 transcript variant X30XM_017006785.1:c.N/AIntron Variant
SETD5 transcript variant X31XM_017006786.1:c.N/AIntron Variant
SETD5 transcript variant X25XM_011533933.1:c.N/AGenic Upstream Transcript Variant
SETD5 transcript variant X5XM_017006768.1:c.N/AGenic Upstream Transcript Variant
SETD5 transcript variant X29XR_001740195.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.656T=0.344
1000GenomesAmericanSub694C=0.970T=0.030
1000GenomesEast AsianSub1008C=1.000T=0.000
1000GenomesEuropeSub1006C=0.999T=0.001
1000GenomesGlobalStudy-wide5008C=0.905T=0.095
1000GenomesSouth AsianSub978C=1.000T=0.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.999T=0.001
The Genome Aggregation DatabaseAfricanSub8684C=0.724T=0.276
The Genome Aggregation DatabaseAmericanSub838C=0.980T=0.020
The Genome Aggregation DatabaseEast AsianSub1622C=1.000T=0.000
The Genome Aggregation DatabaseEuropeSub18494C=0.999T=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29940C=0.918T=0.081
The Genome Aggregation DatabaseOtherSub302C=1.000T=0.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.877T=0.122
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=1.000T=0.000
PMID Title Author Journal
22096494A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.Zuo LPLoS One

P-Value

SNP ID p-value Traits Study
rs64432385.1E-08alcohol dependence22096494

eQTL of rs6443238 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 rs6443238 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 )
chr394364249436486E067-12569
chr394364879436537E067-12518
chr394365449436599E067-12456
chr394366519436708E067-12347
chr394368989436998E067-12057
chr394432499443300E067-5755
chr394438939443996E067-5059
chr394449779445050E067-4005
chr394452529445334E067-3721
chr394453419445395E067-3660
chr394463049446362E067-2693
chr394463679446417E067-2638
chr394464489446643E067-2412
chr394475059447705E067-1350
chr394516949451915E0672639
chr394519879452102E0672932
chr394641049464156E06715049
chr394642989465111E06715243
chr394812099481319E06732154
chr394904169490594E06741361
chr394345359434642E068-14413
chr394432499443300E068-5755
chr394438939443996E068-5059
chr394452529445334E068-3721
chr394453419445395E068-3660
chr394463049446362E068-2693
chr394463679446417E068-2638
chr394464489446643E068-2412
chr394475059447705E068-1350
chr394516949451915E0682639
chr394519879452102E0682932
chr394521149452510E0683059
chr394541229454174E0685067
chr394641049464156E06815049
chr394642989465111E06815243
chr394812099481319E06832154
chr394904169490594E06841361
chr394368989436998E069-12057
chr394432499443300E069-5755
chr394438939443996E069-5059
chr394449779445050E069-4005
chr394452529445334E069-3721
chr394453419445395E069-3660
chr394463049446362E069-2693
chr394463679446417E069-2638
chr394464489446643E069-2412
chr394475059447705E069-1350
chr394546249454700E0695569
chr394626019462863E06913546
chr394631759463237E06914120
chr394641049464156E06915049
chr394642989465111E06915243
chr394904169490594E06941361
chr394345359434642E070-14413
chr394366519436708E070-12347
chr394368989436998E070-12057
chr394432499443300E070-5755
chr394452529445334E070-3721
chr394453419445395E070-3660
chr394475059447705E070-1350
chr394641049464156E07015049
chr394034149403519E071-45536
chr394035429403592E071-45463
chr394364249436486E071-12569
chr394364879436537E071-12518
chr394365449436599E071-12456
chr394366519436708E071-12347
chr394368989436998E071-12057
chr394432499443300E071-5755
chr394452529445334E071-3721
chr394453419445395E071-3660
chr394463049446362E071-2693
chr394463679446417E071-2638
chr394464489446643E071-2412
chr394475059447705E071-1350
chr394584119458482E0719356
chr394626019462863E07113546
chr394641049464156E07115049
chr394642989465111E07115243
chr394812099481319E07132154
chr394904169490594E07141361
chr394432499443300E072-5755
chr394438939443996E072-5059
chr394449779445050E072-4005
chr394452529445334E072-3721
chr394453419445395E072-3660
chr394463049446362E072-2693
chr394463679446417E072-2638
chr394464489446643E072-2412
chr394475059447705E072-1350
chr394516949451915E0722639
chr394519879452102E0722932
chr394521149452510E0723059
chr394577029458329E0728647
chr394584119458482E0729356
chr394812099481319E07232154
chr394904169490594E07241361
chr394364249436486E073-12569
chr394364879436537E073-12518
chr394365449436599E073-12456
chr394366519436708E073-12347
chr394368989436998E073-12057
chr394432499443300E073-5755
chr394438939443996E073-5059
chr394449779445050E073-4005
chr394452529445334E073-3721
chr394453419445395E073-3660
chr394463049446362E073-2693
chr394463679446417E073-2638
chr394464489446643E073-2412
chr394475059447705E073-1350
chr394516949451915E0732639
chr394519879452102E0732932
chr394904169490594E07341361
chr394366519436708E074-12347
chr394368989436998E074-12057
chr394432499443300E074-5755
chr394449779445050E074-4005
chr394452529445334E074-3721
chr394453419445395E074-3660
chr394463049446362E074-2693
chr394463679446417E074-2638
chr394464489446643E074-2412
chr394475059447705E074-1350
chr394527859452867E0743730
chr394528989452975E0743843
chr394541229454174E0745067
chr394626019462863E07413546
chr394631759463237E07414120
chr394641049464156E07415049
chr394642989465111E07415243
chr394668139466918E07417758
chr394812099481319E07432154
chr394904169490594E07441361
chr394368989436998E081-12057
chr394449779445050E081-4005
chr394452529445334E081-3721
chr394453419445395E081-3660
chr394642989465111E08115243
chr394034149403519E082-45536
chr394035429403592E082-45463
chr394463679446417E082-2638
chr394464489446643E082-2412
chr394642989465111E08215243










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr394043389405320E067-43735
chr394053349405415E067-43640
chr394055669405679E067-43376
chr394371269441870E067-7185
chr394043389405320E068-43735
chr394053349405415E068-43640
chr394055669405679E068-43376
chr394371269441870E068-7185
chr394043389405320E069-43735
chr394053349405415E069-43640
chr394055669405679E069-43376
chr394371269441870E069-7185
chr394043389405320E070-43735
chr394053349405415E070-43640
chr394055669405679E070-43376
chr394371269441870E070-7185
chr394036489403778E071-45277
chr394043389405320E071-43735
chr394053349405415E071-43640
chr394371269441870E071-7185
chr394043389405320E072-43735
chr394053349405415E072-43640
chr394055669405679E072-43376
chr394371269441870E072-7185
chr394043389405320E073-43735
chr394053349405415E073-43640
chr394055669405679E073-43376
chr394371269441870E073-7185
chr394043389405320E074-43735
chr394053349405415E074-43640
chr394055669405679E074-43376
chr394371269441870E074-7185
chr394043389405320E081-43735
chr394053349405415E081-43640
chr394055669405679E081-43376
chr394371269441870E081-7185
chr394043389405320E082-43735
chr394053349405415E082-43640
chr394055669405679E082-43376
chr394371269441870E082-7185