rs5761557

Homo sapiens
A>G
HPS4 : Non Coding Transcript Variant
SRRD : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0103 (3112/29984,GnomAD)
A==0121 (3530/29116,TOPMED)
A==0133 (667/5008,1000G)
A==0106 (408/3854,ALSPAC)
A==0105 (390/3708,TWINSUK)
chr22:26482058 (GRCh38.p7) (22q12.1)
AD
GWASdb2
1   publication(s)
See rs on genome
145 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 22NC_000022.11:g.26482058A>G
GRCh37.p13 chr 22NC_000022.10:g.26878024A>G
HPS4 RefSeqGene LRG_590

Gene: HPS4, HPS4, biogenesis of lysosomal organelles complex 3 subunit 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
HPS4 transcript variant 1NM_022081.5:c.N/A5 Prime UTR Variant
HPS4 transcript variant 2NM_152841.2:c.N/AGenic Upstream Transcript Variant
HPS4 transcript variant 5NR_073135.1:n.282T>CT>CNon Coding Transcript Variant
HPS4 transcript variant 6NR_073136.1:n.N/AGenic Upstream Transcript Variant
HPS4 transcript variant X1XM_011530485.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X16XM_011530492.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X2XM_011530486.2:c.N/A5 Prime UTR Variant
HPS4 transcript variant X3XM_011530487.2:c.N/A5 Prime UTR Variant
HPS4 transcript variant X5XM_011530488.2:c.N/A5 Prime UTR Variant
HPS4 transcript variant X6XM_011530489.2:c.N/A5 Prime UTR Variant
HPS4 transcript variant X7XM_011530490.2:c.N/A5 Prime UTR Variant
HPS4 transcript variant X8XM_006724353.3:c.N/A5 Prime UTR Variant
HPS4 transcript variant X9XM_006724354.3:c.N/A5 Prime UTR Variant
HPS4 transcript variant X11XM_011530491.2:c.N/A5 Prime UTR Variant
HPS4 transcript variant X12XM_017029042.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X13XM_017029043.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X14XM_017029044.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X17XM_011530493.2:c.N/A5 Prime UTR Variant
HPS4 transcript variant X18XM_017029045.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X19XM_017029046.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X20XM_017029047.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X21XM_017029048.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X22XM_017029049.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X23XM_017029050.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X24XM_017029051.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X26XM_017029052.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X28XM_017029054.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X32XM_017029055.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X34XM_017029056.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X35XM_017029057.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X37XM_017029058.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X38XM_017029059.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X39XM_017029060.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X40XM_017029061.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X41XM_017029062.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X42XM_017029063.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X43XM_017029064.1:c.N/A5 Prime UTR Variant
HPS4 transcript variant X19XM_006724360.3:c.N/AGenic Upstream Transcript Variant
HPS4 transcript variant X20XM_011530494.2:c.N/AGenic Upstream Transcript Variant
HPS4 transcript variant X21XM_011530495.2:c.N/AGenic Upstream Transcript Variant
HPS4 transcript variant X23XM_011530496.2:c.N/AGenic Upstream Transcript Variant
HPS4 transcript variant X18XM_017029053.1:c.N/AGenic Upstream Transcript Variant
HPS4 transcript variant X4XR_937947.1:n.364T>CT>CNon Coding Transcript Variant
HPS4 transcript variant X10XR_001755361.1:n....XR_001755361.1:n.364T>CT>CNon Coding Transcript Variant
HPS4 transcript variant X15XR_001755362.1:n....XR_001755362.1:n.364T>CT>CNon Coding Transcript Variant
HPS4 transcript variant X16XR_001755364.1:n....XR_001755364.1:n.269T>CT>CNon Coding Transcript Variant
HPS4 transcript variant X36XR_001755366.1:n....XR_001755366.1:n.273T>CT>CNon Coding Transcript Variant

Gene: SRRD, SRR1 domain containing(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
SRRD transcriptNM_001013694.2:c.N/AUpstream Transcript Variant
SRRD transcript variant X1XM_011530178.2:c.N/AUpstream Transcript Variant
SRRD transcript variant X2XM_017028799.1:c.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.120G=0.880
1000GenomesAmericanSub694A=0.260G=0.740
1000GenomesEast AsianSub1008A=0.139G=0.861
1000GenomesEuropeSub1006A=0.080G=0.920
1000GenomesGlobalStudy-wide5008A=0.133G=0.867
1000GenomesSouth AsianSub978A=0.110G=0.890
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.106G=0.894
The Genome Aggregation DatabaseAfricanSub8728A=0.131G=0.869
The Genome Aggregation DatabaseAmericanSub838A=0.310G=0.690
The Genome Aggregation DatabaseEast AsianSub1618A=0.164G=0.836
The Genome Aggregation DatabaseEuropeSub18498A=0.076G=0.924
The Genome Aggregation DatabaseGlobalStudy-wide29984A=0.103G=0.896
The Genome Aggregation DatabaseOtherSub302A=0.140G=0.860
Trans-Omics for Precision MedicineGlobalStudy-wide29116A=0.121G=0.878
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.105G=0.895
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs57615570.00084alcohol dependence20201924

eQTL of rs5761557 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 rs5761557 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 )
chr222683038426830434E067-47590
chr222685815626858370E067-19654
chr222687644426876585E067-1439
chr222687709526877322E067-702
chr222687739926877504E067-520
chr222687765926878175E0670
chr222687817726878486E067153
chr222688161126881674E0673587
chr222688176526881892E0673741
chr222688191726882087E0673893
chr222689851326899651E06720489
chr222690676526906805E06728741
chr222690696326907155E06728939
chr222690970426909789E06731680
chr222690983826910308E06731814
chr222691038526910456E06732361
chr222691168226912478E06733658
chr222685680426857608E068-20416
chr222685815626858370E068-19654
chr222685843426860085E068-17939
chr222687644426876585E068-1439
chr222687709526877322E068-702
chr222687739926877504E068-520
chr222687765926878175E0680
chr222687817726878486E068153
chr222688081326881400E0682789
chr222689851326899651E06820489
chr222689970426900317E06821680
chr222690059026900635E06822566
chr222684923826849607E069-28417
chr222685843426860085E069-17939
chr222687644426876585E069-1439
chr222687709526877322E069-702
chr222687739926877504E069-520
chr222687765926878175E0690
chr222687817726878486E069153
chr222688081326881400E0692789
chr222688161126881674E0693587
chr222688176526881892E0693741
chr222688191726882087E0693893
chr222689851326899651E06920489
chr222689970426900317E06921680
chr222690970426909789E06931680
chr222690983826910308E06931814
chr222687644426876585E070-1439
chr222687709526877322E070-702
chr222688081326881400E0702789
chr222690676526906805E07028741
chr222690696326907155E07028939
chr222690970426909789E07031680
chr222685815626858370E071-19654
chr222687644426876585E071-1439
chr222687709526877322E071-702
chr222687739926877504E071-520
chr222687765926878175E0710
chr222687817726878486E071153
chr222688081326881400E0712789
chr222688161126881674E0713587
chr222688176526881892E0713741
chr222690676526906805E07128741
chr222690696326907155E07128939
chr222692363626924410E07145612
chr222686030826860727E072-17297
chr222687644426876585E072-1439
chr222687709526877322E072-702
chr222687739926877504E072-520
chr222687765926878175E0720
chr222688081326881400E0722789
chr222688161126881674E0723587
chr222688176526881892E0723741
chr222690676526906805E07228741
chr222690696326907155E07228939
chr222690983826910308E07231814
chr222683271026833288E073-44736
chr222683330926833467E073-44557
chr222684228726842381E073-35643
chr222684402426844074E073-33950
chr222684413826844192E073-33832
chr222684923826849607E073-28417
chr222685843426860085E073-17939
chr222687272026873597E073-4427
chr222687644426876585E073-1439
chr222687709526877322E073-702
chr222687739926877504E073-520
chr222687765926878175E0730
chr222687817726878486E073153
chr222688081326881400E0732789
chr222688161126881674E0733587
chr222688176526881892E0733741
chr222688191726882087E0733893
chr222689851326899651E07320489
chr222692336226923520E07345338
chr222692363626924410E07345612
chr222687644426876585E074-1439
chr222687709526877322E074-702
chr222687739926877504E074-520
chr222687765926878175E0740
chr222687817726878486E074153
chr222688081326881400E0742789
chr222688521126885265E0747187
chr222688539426885808E0747370
chr222690970426909789E07431680
chr222683244226832544E081-45480
chr222683271026833288E081-44736
chr222683330926833467E081-44557
chr222683368126833731E081-44293
chr222683381026833860E081-44164
chr222683407926834282E081-43742
chr222684402426844074E081-33950
chr222684413826844192E081-33832
chr222684765026848052E081-29972
chr222685596826856701E081-21323
chr222685680426857608E081-20416
chr222685771626857824E081-20200
chr222685798626858062E081-19962
chr222685815626858370E081-19654
chr222685843426860085E081-17939
chr222686128726861375E081-16649
chr222686178726862498E081-15526
chr222686280726862870E081-15154
chr222687644426876585E081-1439
chr222687709526877322E081-702
chr222687765926878175E0810
chr222687817726878486E081153
chr222690983826910308E08131814
chr222691038526910456E08132361
chr222691078126910831E08132757
chr222691084726910927E08132823
chr222692336226923520E08145338
chr222692363626924410E08145612
chr222683330926833467E082-44557
chr222683368126833731E082-44293
chr222684402426844074E082-33950
chr222684413826844192E082-33832
chr222685843426860085E082-17939
chr222686128726861375E082-16649
chr222686178726862498E082-15526
chr222686280726862870E082-15154
chr222687644426876585E082-1439
chr222687709526877322E082-702
chr222687739926877504E082-520
chr222688161126881674E0823587
chr222688176526881892E0823741
chr222688191726882087E0823893
chr222690970426909789E08231680










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr222687896026880719E067936
chr222690795926908938E06729935
chr222687896026880719E068936
chr222690795926908938E06829935
chr222687896026880719E069936
chr222690795926908938E06929935
chr222687896026880719E070936
chr222690795926908938E07029935
chr222687896026880719E071936
chr222690795926908938E07129935
chr222687896026880719E072936
chr222690795926908938E07229935
chr222687896026880719E073936
chr222690795926908938E07329935
chr222687896026880719E074936
chr222690795926908938E07429935
chr222687896026880719E081936
chr222690795926908938E08129935
chr222687896026880719E082936
chr222690795926908938E08229935