rs2854992

Homo sapiens
A>G
PSAP : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0234 (6997/29876,GnomAD)
A==0221 (6454/29118,TOPMED)
A==0211 (1057/5008,1000G)
A==0236 (909/3854,ALSPAC)
A==0244 (905/3708,TWINSUK)
chr10:71826828 (GRCh38.p7) (10q22.1)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.71826828A>G
GRCh37.p13 chr 10NC_000010.10:g.73586585A>G
PSAP RefSeqGeneNG_009301.1:g.29498T>C

Gene: PSAP, prosaposin(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PSAP transcript variant 2NM_001042465.2:c.N/AIntron Variant
PSAP transcript variant 3NM_001042466.2:c.N/AIntron Variant
PSAP transcript variant 1NM_002778.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.134G=0.866
1000GenomesAmericanSub694A=0.300G=0.700
1000GenomesEast AsianSub1008A=0.251G=0.749
1000GenomesEuropeSub1006A=0.239G=0.761
1000GenomesGlobalStudy-wide5008A=0.211G=0.789
1000GenomesSouth AsianSub978A=0.190G=0.810
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.236G=0.764
The Genome Aggregation DatabaseAfricanSub8706A=0.152G=0.848
The Genome Aggregation DatabaseAmericanSub836A=0.230G=0.770
The Genome Aggregation DatabaseEast AsianSub1618A=0.206G=0.794
The Genome Aggregation DatabaseEuropeSub18416A=0.275G=0.724
The Genome Aggregation DatabaseGlobalStudy-wide29876A=0.234G=0.765
The Genome Aggregation DatabaseOtherSub300A=0.280G=0.720
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.221G=0.778
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.244G=0.756
PMID Title Author Journal
22072270Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms.Wang KSJ Neural Transm (Vienna)

P-Value

SNP ID p-value Traits Study
rs28549923.81E-05alcohol withdrawal symptoms22072270

eQTL of rs2854992 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 rs2854992 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 )
chr107357166373572152E067-14433
chr107357217973572806E067-13779
chr107357400473574191E067-12394
chr107357430773574387E067-12198
chr107357450373574598E067-11987
chr107357513373575278E067-11307
chr107357535773575638E067-10947
chr107357577873575828E067-10757
chr107357589873575985E067-10600
chr107357599073576050E067-10535
chr107357620373576306E067-10279
chr107357633473576384E067-10201
chr107357644073576500E067-10085
chr107357651173576597E067-9988
chr107357665173576701E067-9884
chr107357683173577310E067-9275
chr107357734773577459E067-9126
chr107357757373578109E067-8476
chr107357819573578385E067-8200
chr107357843573578487E067-8098
chr107357852973578662E067-7923
chr107357883373578899E067-7686
chr107358250073582566E067-4019
chr107358264173582691E067-3894
chr107358292873583032E067-3553
chr107358309473583187E067-3398
chr107358332473583376E067-3209
chr107358360773583885E067-2700
chr107358406473584145E067-2440
chr107358777773587918E0671192
chr107359171673592023E0675131
chr107359205573592329E0675470
chr107359238073592461E0675795
chr107359332573593411E0676740
chr107359342673593509E0676841
chr107359383173593933E0677246
chr107359397773594073E0677392
chr107359423873594304E0677653
chr107359440773594507E0677822
chr107359525173595305E0678666
chr107359532373595373E0678738
chr107359540673595540E0678821
chr107359559173599020E0679006
chr107360120273601267E06714617
chr107360136073601420E06714775
chr107360180773601870E06715222
chr107360191773602024E06715332
chr107360207473602118E06715489
chr107360230073602432E06715715
chr107360257973602629E06715994
chr107360265373602902E06716068
chr107360294073603371E06716355
chr107360342573603502E06716840
chr107360354873603683E06716963
chr107360392773603986E06717342
chr107360401673604070E06717431
chr107360526773605360E06718682
chr107360542173605680E06718836
chr107360587473606207E06719289
chr107360659773606871E06720012
chr107360712273607319E06720537
chr107360734773607401E06720762
chr107361377473614153E06727189
chr107361416373614238E06727578
chr107361928573619552E06732700
chr107361963273619761E06733047
chr107361982973621045E06733244
chr107362118673621306E06734601
chr107357090273571234E068-15351
chr107357166373572152E068-14433
chr107357217973572806E068-13779
chr107357577873575828E068-10757
chr107357589873575985E068-10600
chr107357599073576050E068-10535
chr107357620373576306E068-10279
chr107357633473576384E068-10201
chr107357644073576500E068-10085
chr107357651173576597E068-9988
chr107357665173576701E068-9884
chr107357683173577310E068-9275
chr107357734773577459E068-9126
chr107357757373578109E068-8476
chr107357819573578385E068-8200
chr107357843573578487E068-8098
chr107357852973578662E068-7923
chr107357883373578899E068-7686
chr107358332473583376E068-3209
chr107359100473591054E0684419
chr107359108873591421E0684503
chr107359154773591601E0684962
chr107359171673592023E0685131
chr107359205573592329E0685470
chr107359238073592461E0685795
chr107359281673592999E0686231
chr107359307173593121E0686486
chr107359332573593411E0686740
chr107359342673593509E0686841
chr107359383173593933E0687246
chr107359397773594073E0687392
chr107359423873594304E0687653
chr107359440773594507E0687822
chr107359525173595305E0688666
chr107359532373595373E0688738
chr107359540673595540E0688821
chr107359930573599459E06812720
chr107360120273601267E06814617
chr107360136073601420E06814775
chr107360180773601870E06815222
chr107360191773602024E06815332
chr107360207473602118E06815489
chr107360230073602432E06815715
chr107360342573603502E06816840
chr107360354873603683E06816963
chr107360392773603986E06817342
chr107360401673604070E06817431
chr107360505573605129E06818470
chr107360526773605360E06818682
chr107360542173605680E06818836
chr107360587473606207E06819289
chr107360659773606871E06820012
chr107361963273619761E06833047
chr107362118673621306E06834601
chr107362747973628435E06840894
chr107357166373572152E069-14433
chr107357217973572806E069-13779
chr107357283373572890E069-13695
chr107357577873575828E069-10757
chr107357589873575985E069-10600
chr107357599073576050E069-10535
chr107357620373576306E069-10279
chr107357633473576384E069-10201
chr107357644073576500E069-10085
chr107357651173576597E069-9988
chr107357665173576701E069-9884
chr107357683173577310E069-9275
chr107357734773577459E069-9126
chr107357757373578109E069-8476
chr107357819573578385E069-8200
chr107357843573578487E069-8098
chr107357852973578662E069-7923
chr107358292873583032E069-3553
chr107358309473583187E069-3398
chr107358332473583376E069-3209
chr107358360773583885E069-2700
chr107358406473584145E069-2440
chr107358753673587606E069951
chr107358768673587737E0691101
chr107358777773587918E0691192
chr107359100473591054E0694419
chr107359108873591421E0694503
chr107359154773591601E0694962
chr107359171673592023E0695131
chr107359205573592329E0695470
chr107359238073592461E0695795
chr107359281673592999E0696231
chr107359307173593121E0696486
chr107359332573593411E0696740
chr107359342673593509E0696841
chr107359383173593933E0697246
chr107359397773594073E0697392
chr107359423873594304E0697653
chr107359440773594507E0697822
chr107359525173595305E0698666
chr107359532373595373E0698738
chr107359540673595540E0698821
chr107359559173599020E0699006
chr107359930573599459E06912720
chr107360080173601080E06914216
chr107360120273601267E06914617
chr107360136073601420E06914775
chr107360180773601870E06915222
chr107360191773602024E06915332
chr107360207473602118E06915489
chr107360230073602432E06915715
chr107360257973602629E06915994
chr107360265373602902E06916068
chr107360294073603371E06916355
chr107360342573603502E06916840
chr107360354873603683E06916963
chr107360392773603986E06917342
chr107360526773605360E06918682
chr107360542173605680E06918836
chr107360659773606871E06920012
chr107360712273607319E06920537
chr107360734773607401E06920762
chr107360760373607655E06921018
chr107360769273607790E06921107
chr107361170873612613E06925123
chr107361377473614153E06927189
chr107361416373614238E06927578
chr107361928573619552E06932700
chr107361963273619761E06933047
chr107361982973621045E06933244
chr107362118673621306E06934601
chr107362747973628435E06940894
chr107356429473564382E070-22203
chr107356445373564503E070-22082
chr107356465273564702E070-21883
chr107356473773564828E070-21757
chr107359332573593411E0706740
chr107359342673593509E0706841
chr107359383173593933E0707246
chr107359397773594073E0707392
chr107359423873594304E0707653
chr107359559173599020E0709006
chr107359930573599459E07012720
chr107360080173601080E07014216
chr107360120273601267E07014617
chr107360136073601420E07014775
chr107360542173605680E07018836
chr107360587473606207E07019289
chr107360659773606871E07020012
chr107360712273607319E07020537
chr107360734773607401E07020762
chr107360760373607655E07021018
chr107360769273607790E07021107
chr107361928573619552E07032700
chr107361963273619761E07033047
chr107361982973621045E07033244
chr107355686473558261E071-28324
chr107357166373572152E071-14433
chr107357217973572806E071-13779
chr107357283373572890E071-13695
chr107357535773575638E071-10947
chr107357577873575828E071-10757
chr107357589873575985E071-10600
chr107357599073576050E071-10535
chr107357620373576306E071-10279
chr107357633473576384E071-10201
chr107357644073576500E071-10085
chr107357651173576597E071-9988
chr107357665173576701E071-9884
chr107357683173577310E071-9275
chr107357734773577459E071-9126
chr107357757373578109E071-8476
chr107357819573578385E071-8200
chr107357843573578487E071-8098
chr107357852973578662E071-7923
chr107357883373578899E071-7686
chr107357905673579218E071-7367
chr107358292873583032E071-3553
chr107358309473583187E071-3398
chr107358332473583376E071-3209
chr107358360773583885E071-2700
chr107358406473584145E071-2440
chr107358466573584782E071-1803
chr107358486573584915E071-1670
chr107358494673585048E071-1537
chr107358513373585270E071-1315
chr107359205573592329E0715470
chr107359238073592461E0715795
chr107359281673592999E0716231
chr107359307173593121E0716486
chr107359332573593411E0716740
chr107359342673593509E0716841
chr107359383173593933E0717246
chr107359397773594073E0717392
chr107359423873594304E0717653
chr107359525173595305E0718666
chr107359532373595373E0718738
chr107359540673595540E0718821
chr107359559173599020E0719006
chr107359930573599459E07112720
chr107360120273601267E07114617
chr107360136073601420E07114775
chr107360180773601870E07115222
chr107360191773602024E07115332
chr107360207473602118E07115489
chr107360230073602432E07115715
chr107360257973602629E07115994
chr107360265373602902E07116068
chr107360294073603371E07116355
chr107360342573603502E07116840
chr107360354873603683E07116963
chr107360392773603986E07117342
chr107360401673604070E07117431
chr107360505573605129E07118470
chr107360526773605360E07118682
chr107360542173605680E07118836
chr107360587473606207E07119289
chr107360659773606871E07120012
chr107360712273607319E07120537
chr107360734773607401E07120762
chr107361377473614153E07127189
chr107361416373614238E07127578
chr107361799173618374E07131406
chr107361848573618549E07131900
chr107361928573619552E07132700
chr107361963273619761E07133047
chr107361982973621045E07133244
chr107362118673621306E07134601
chr107362131073621482E07134725
chr107362747973628435E07140894
chr107357166373572152E072-14433
chr107357217973572806E072-13779
chr107357535773575638E072-10947
chr107357577873575828E072-10757
chr107357589873575985E072-10600
chr107357599073576050E072-10535
chr107357620373576306E072-10279
chr107357633473576384E072-10201
chr107357644073576500E072-10085
chr107357651173576597E072-9988
chr107357665173576701E072-9884
chr107357683173577310E072-9275
chr107357734773577459E072-9126
chr107357757373578109E072-8476
chr107357819573578385E072-8200
chr107357843573578487E072-8098
chr107357852973578662E072-7923
chr107357883373578899E072-7686
chr107357905673579218E072-7367
chr107357922973579314E072-7271
chr107358292873583032E072-3553
chr107358309473583187E072-3398
chr107358332473583376E072-3209
chr107358360773583885E072-2700
chr107358406473584145E072-2440
chr107359154773591601E0724962
chr107359171673592023E0725131
chr107359205573592329E0725470
chr107359238073592461E0725795
chr107359281673592999E0726231
chr107359307173593121E0726486
chr107359332573593411E0726740
chr107359342673593509E0726841
chr107359383173593933E0727246
chr107359397773594073E0727392
chr107359423873594304E0727653
chr107359525173595305E0728666
chr107359532373595373E0728738
chr107359540673595540E0728821
chr107359559173599020E0729006
chr107359930573599459E07212720
chr107360080173601080E07214216
chr107360120273601267E07214617
chr107360136073601420E07214775
chr107360180773601870E07215222
chr107360191773602024E07215332
chr107360207473602118E07215489
chr107360230073602432E07215715
chr107360257973602629E07215994
chr107360265373602902E07216068
chr107360294073603371E07216355
chr107360342573603502E07216840
chr107360354873603683E07216963
chr107360392773603986E07217342
chr107360401673604070E07217431
chr107360505573605129E07218470
chr107360526773605360E07218682
chr107360542173605680E07218836
chr107360587473606207E07219289
chr107360659773606871E07220012
chr107360712273607319E07220537
chr107360734773607401E07220762
chr107361377473614153E07227189
chr107361416373614238E07227578
chr107361928573619552E07232700
chr107361963273619761E07233047
chr107361982973621045E07233244
chr107362118673621306E07234601
chr107362131073621482E07234725
chr107357166373572152E073-14433
chr107357577873575828E073-10757
chr107357589873575985E073-10600
chr107357599073576050E073-10535
chr107357620373576306E073-10279
chr107357633473576384E073-10201
chr107357644073576500E073-10085
chr107357651173576597E073-9988
chr107357665173576701E073-9884
chr107357683173577310E073-9275
chr107357734773577459E073-9126
chr107357757373578109E073-8476
chr107357819573578385E073-8200
chr107357843573578487E073-8098
chr107357852973578662E073-7923
chr107357883373578899E073-7686
chr107357905673579218E073-7367
chr107358777773587918E0731192
chr107358830173588351E0731716
chr107358852873588578E0731943
chr107358862273588878E0732037
chr107359154773591601E0734962
chr107359171673592023E0735131
chr107359205573592329E0735470
chr107359238073592461E0735795
chr107359281673592999E0736231
chr107359307173593121E0736486
chr107359332573593411E0736740
chr107359342673593509E0736841
chr107359383173593933E0737246
chr107359397773594073E0737392
chr107359423873594304E0737653
chr107359525173595305E0738666
chr107359532373595373E0738738
chr107359540673595540E0738821
chr107359559173599020E0739006
chr107359930573599459E07312720
chr107360080173601080E07314216
chr107360120273601267E07314617
chr107360136073601420E07314775
chr107360180773601870E07315222
chr107360191773602024E07315332
chr107360207473602118E07315489
chr107360230073602432E07315715
chr107360294073603371E07316355
chr107360342573603502E07316840
chr107360354873603683E07316963
chr107360505573605129E07318470
chr107360526773605360E07318682
chr107360542173605680E07318836
chr107360659773606871E07320012
chr107360712273607319E07320537
chr107360734773607401E07320762
chr107361982973621045E07333244
chr107362118673621306E07334601
chr107362131073621482E07334725
chr107362747973628435E07340894
chr107354222373542305E074-44280
chr107354237373542424E074-44161
chr107354275873542927E074-43658
chr107356495673565071E074-21514
chr107356516773566311E074-20274
chr107357535773575638E074-10947
chr107357577873575828E074-10757
chr107357589873575985E074-10600
chr107357599073576050E074-10535
chr107357620373576306E074-10279
chr107357633473576384E074-10201
chr107357644073576500E074-10085
chr107357651173576597E074-9988
chr107357665173576701E074-9884
chr107357683173577310E074-9275
chr107357734773577459E074-9126
chr107357757373578109E074-8476
chr107357819573578385E074-8200
chr107357843573578487E074-8098
chr107357852973578662E074-7923
chr107357883373578899E074-7686
chr107357905673579218E074-7367
chr107358292873583032E074-3553
chr107358309473583187E074-3398
chr107358332473583376E074-3209
chr107358360773583885E074-2700
chr107359022473590976E0743639
chr107359100473591054E0744419
chr107359108873591421E0744503
chr107359154773591601E0744962
chr107359171673592023E0745131
chr107359205573592329E0745470
chr107359238073592461E0745795
chr107359281673592999E0746231
chr107359307173593121E0746486
chr107359332573593411E0746740
chr107359342673593509E0746841
chr107359383173593933E0747246
chr107359397773594073E0747392
chr107359423873594304E0747653
chr107359440773594507E0747822
chr107359525173595305E0748666
chr107359532373595373E0748738
chr107359540673595540E0748821
chr107359559173599020E0749006
chr107359930573599459E07412720
chr107360080173601080E07414216
chr107360120273601267E07414617
chr107360136073601420E07414775
chr107360180773601870E07415222
chr107360191773602024E07415332
chr107360207473602118E07415489
chr107360230073602432E07415715
chr107360257973602629E07415994
chr107360265373602902E07416068
chr107360294073603371E07416355
chr107360342573603502E07416840
chr107360354873603683E07416963
chr107360392773603986E07417342
chr107360401673604070E07417431
chr107360461073604723E07418025
chr107360505573605129E07418470
chr107360526773605360E07418682
chr107360542173605680E07418836
chr107360587473606207E07419289
chr107360659773606871E07420012
chr107360712273607319E07420537
chr107360734773607401E07420762
chr107360760373607655E07421018
chr107360769273607790E07421107
chr107361170873612613E07425123
chr107361377473614153E07427189
chr107361416373614238E07427578
chr107361431573614359E07427730
chr107361928573619552E07432700
chr107361963273619761E07433047
chr107361982973621045E07433244
chr107362118673621306E07434601
chr107356377173564237E081-22348
chr107356429473564382E081-22203
chr107356445373564503E081-22082
chr107356682873566912E081-19673
chr107357620373576306E081-10279
chr107357633473576384E081-10201
chr107357644073576500E081-10085
chr107357651173576597E081-9988
chr107357665173576701E081-9884
chr107357683173577310E081-9275
chr107357734773577459E081-9126
chr107359559173599020E0819006
chr107359930573599459E08112720
chr107359971473600627E08113129
chr107360080173601080E08114216
chr107360120273601267E08114617
chr107360136073601420E08114775
chr107360180773601870E08115222
chr107360191773602024E08115332
chr107360207473602118E08115489
chr107360265373602902E08116068
chr107360294073603371E08116355
chr107360659773606871E08120012
chr107360712273607319E08120537
chr107360734773607401E08120762
chr107360760373607655E08121018
chr107360769273607790E08121107
chr107360783773608002E08121252
chr107360891773609124E08122332
chr107356377173564237E082-22348
chr107359540673595540E0828821
chr107359559173599020E0829006
chr107360080173601080E08214216
chr107360120273601267E08214617
chr107360136073601420E08214775
chr107360257973602629E08215994
chr107360265373602902E08216068
chr107360294073603371E08216355
chr107360542173605680E08218836
chr107360734773607401E08220762
chr107360760373607655E08221018
chr107360769273607790E08221107
chr107360783773608002E08221252










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr107360992473611623E06723339
chr107360992473611623E06823339
chr107360992473611623E06923339
chr107360992473611623E07023339
chr107360992473611623E07123339
chr107360992473611623E07223339
chr107360992473611623E07323339
chr107360992473611623E07423339
chr107360992473611623E08123339
chr107360992473611623E08223339