rs177820

Homo sapiens
A>G
NFATC1 : Intron Variant
LOC102723506 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0367 (11007/29932,GnomAD)
G=0376 (10957/29118,TOPMED)
G=0477 (2390/5008,1000G)
G=0358 (1380/3854,ALSPAC)
G=0371 (1375/3708,TWINSUK)
chr18:79516964 (GRCh38.p7) (18q23)
AD
GWASdb2
4   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 18NC_000018.10:g.79516964A>G
GRCh37.p13 chr 18NC_000018.9:g.77276964A>G
NFATC1 RefSeqGeneNG_029226.1:g.126193A>G

Gene: NFATC1, nuclear factor of activated T-cells 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
NFATC1 transcript variant 6NM_001278669.1:c.N/AIntron Variant
NFATC1 transcript variant 7NM_001278670.1:c.N/AIntron Variant
NFATC1 transcript variant 8NM_001278672.1:c.N/AIntron Variant
NFATC1 transcript variant 10NM_001278673.1:c.N/AIntron Variant
NFATC1 transcript variant 2NM_006162.4:c.N/AIntron Variant
NFATC1 transcript variant 3NM_172387.2:c.N/AIntron Variant
NFATC1 transcript variant 4NM_172388.2:c.N/AIntron Variant
NFATC1 transcript variant 5NM_172389.2:c.N/AIntron Variant
NFATC1 transcript variant 9NM_001278675.1:c.N/AGenic Downstream Transcript Variant
NFATC1 transcript variant 1NM_172390.2:c.N/AGenic Downstream Transcript Variant
NFATC1 transcript variant X1XM_017025783.1:c.N/AGenic Downstream Transcript Variant

Gene: LOC102723506, uncharacterized LOC102723506(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC102723506 transcript variant X1XR_935689.1:n.768...XR_935689.1:n.7686T>CT>CNon Coding Transcript Variant
LOC102723506 transcript variant X2XR_001753516.1:n....XR_001753516.1:n.6987T>CT>CNon Coding Transcript Variant
LOC102723506 transcript variant X3XR_001753517.1:n....XR_001753517.1:n.7690T>CT>CNon Coding Transcript Variant
LOC102723506 transcript variant X4XR_935690.2:n.691...XR_935690.2:n.6916T>CT>CNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.663G=0.337
1000GenomesAmericanSub694A=0.560G=0.440
1000GenomesEast AsianSub1008A=0.276G=0.724
1000GenomesEuropeSub1006A=0.644G=0.356
1000GenomesGlobalStudy-wide5008A=0.523G=0.477
1000GenomesSouth AsianSub978A=0.430G=0.570
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.642G=0.358
The Genome Aggregation DatabaseAfricanSub8720A=0.650G=0.350
The Genome Aggregation DatabaseAmericanSub838A=0.520G=0.480
The Genome Aggregation DatabaseEast AsianSub1610A=0.278G=0.722
The Genome Aggregation DatabaseEuropeSub18462A=0.660G=0.339
The Genome Aggregation DatabaseGlobalStudy-wide29932A=0.632G=0.367
The Genome Aggregation DatabaseOtherSub302A=0.600G=0.400
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.623G=0.376
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.629G=0.371
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
19619005Candidate gene analysis of femoral neck trabecular and cortical volumetric bone mineral density in older men.Yerges LMJ Bone Miner Res
20357209Molecular genetic studies of gene identification for osteoporosis: the 2009 update.Xu XHEndocr Rev
19453261High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.Yerges LMJ Bone Miner Res

P-Value

SNP ID p-value Traits Study
rs1778200.000924alcohol dependence20201924

eQTL of rs177820 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 rs177820 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 )
chr187723672277236913E067-40051
chr187723692377237204E067-39760
chr187723720677237575E067-39389
chr187723764677237707E067-39257
chr187726848977268688E067-8276
chr187727979277280124E0672828
chr187728015377280704E0673189
chr187728568277285749E0678718
chr187728575377285951E0678789
chr187728596577286440E0679001
chr187728650777287079E0679543
chr187729249877292864E06715534
chr187729291477293053E06715950
chr187729993877299988E06722974
chr187730012177300175E06723157
chr187730036577300415E06723401
chr187730054277300928E06723578
chr187730096977301019E06724005
chr187730121977301259E06724255
chr187730137477301490E06724410
chr187730282577302906E06725861
chr187725653577258114E068-18850
chr187726618277266328E068-10636
chr187728015377280704E0683189
chr187728575377285951E0688789
chr187728596577286440E0689001
chr187728650777287079E0689543
chr187728869077289539E06811726
chr187729929277299407E06822328
chr187729945577299532E06822491
chr187729969877299760E06822734
chr187729993877299988E06822974
chr187730012177300175E06823157
chr187730036577300415E06823401
chr187730054277300928E06823578
chr187730096977301019E06824005
chr187730121977301259E06824255
chr187730137477301490E06824410
chr187730323877303311E06826274
chr187730341177303679E06826447
chr187730368277303739E06826718
chr187730386277303912E06826898
chr187730765377307703E06830689
chr187730780477307854E06830840
chr187730788877307930E06830924
chr187730801377308063E06831049
chr187730810677308150E06831142
chr187723672277236913E069-40051
chr187723692377237204E069-39760
chr187723720677237575E069-39389
chr187723764677237707E069-39257
chr187725155477252117E069-24847
chr187725215077252328E069-24636
chr187725653577258114E069-18850
chr187726618277266328E069-10636
chr187728845277288609E06911488
chr187728869077289539E06911726
chr187729249877292864E06915534
chr187729291477293053E06915950
chr187729993877299988E06922974
chr187730012177300175E06923157
chr187730036577300415E06923401
chr187730054277300928E06923578
chr187730096977301019E06924005
chr187730121977301259E06924255
chr187730137477301490E06924410
chr187730282577302906E06925861
chr187730323877303311E06926274
chr187730341177303679E06926447
chr187730368277303739E06926718
chr187730386277303912E06926898
chr187730413277304340E06927168
chr187730434577304431E06927381
chr187730743577307597E06930471
chr187730765377307703E06930689
chr187730780477307854E06930840
chr187730788877307930E06930924
chr187730801377308063E06931049
chr187730810677308150E06931142
chr187732040577320458E06943441
chr187732058277320632E06943618
chr187732086077320956E06943896
chr187722742877227494E070-49470
chr187722754377227715E070-49249
chr187722824877228414E070-48550
chr187722850077228712E070-48252
chr187722905177229121E070-47843
chr187722964277229729E070-47235
chr187722990177229959E070-47005
chr187722999277230077E070-46887
chr187723011477230357E070-46607
chr187723040277230560E070-46404
chr187723062877230761E070-46203
chr187723151177231621E070-45343
chr187723167377232012E070-44952
chr187725653577258114E070-18850
chr187726255177262602E070-14362
chr187726618277266328E070-10636
chr187726848977268688E070-8276
chr187726889777269028E070-7936
chr187726971777269794E070-7170
chr187727979277280124E0702828
chr187728015377280704E0703189
chr187728575377285951E0708789
chr187728596577286440E0709001
chr187728650777287079E0709543
chr187728711877287250E07010154
chr187728727377287345E07010309
chr187728740177287455E07010437
chr187728753677287646E07010572
chr187728765677287722E07010692
chr187728777377287908E07010809
chr187728801377288148E07011049
chr187728819177288288E07011227
chr187728845277288609E07011488
chr187729249877292864E07015534
chr187729291477293053E07015950
chr187730054277300928E07023578
chr187730096977301019E07024005
chr187730121977301259E07024255
chr187730137477301490E07024410
chr187730678777306896E07029823
chr187730692577307273E07029961
chr187730743577307597E07030471
chr187723720677237575E071-39389
chr187723764677237707E071-39257
chr187725155477252117E071-24847
chr187725653577258114E071-18850
chr187726618277266328E071-10636
chr187726848977268688E071-8276
chr187728015377280704E0713189
chr187728568277285749E0718718
chr187729249877292864E07115534
chr187729291477293053E07115950
chr187729929277299407E07122328
chr187729945577299532E07122491
chr187729969877299760E07122734
chr187729993877299988E07122974
chr187730012177300175E07123157
chr187730036577300415E07123401
chr187730054277300928E07123578
chr187730282577302906E07125861
chr187730323877303311E07126274
chr187730341177303679E07126447
chr187730368277303739E07126718
chr187730386277303912E07126898
chr187730413277304340E07127168
chr187730743577307597E07130471
chr187730765377307703E07130689
chr187730780477307854E07130840
chr187730788877307930E07130924
chr187723672277236913E072-40051
chr187723692377237204E072-39760
chr187723720677237575E072-39389
chr187723764677237707E072-39257
chr187723796377238046E072-38918
chr187725155477252117E072-24847
chr187725215077252328E072-24636
chr187725579677255881E072-21083
chr187725596877256077E072-20887
chr187725615577256446E072-20518
chr187725653577258114E072-18850
chr187726618277266328E072-10636
chr187727979277280124E0722828
chr187728568277285749E0728718
chr187728650777287079E0729543
chr187729291477293053E07215950
chr187729969877299760E07222734
chr187729993877299988E07222974
chr187730012177300175E07223157
chr187730036577300415E07223401
chr187730054277300928E07223578
chr187730282577302906E07225861
chr187730323877303311E07226274
chr187730341177303679E07226447
chr187730368277303739E07226718
chr187730386277303912E07226898
chr187730413277304340E07227168
chr187730434577304431E07227381
chr187730743577307597E07230471
chr187730765377307703E07230689
chr187732040577320458E07243441
chr187732058277320632E07243618
chr187726618277266328E073-10636
chr187728568277285749E0738718
chr187730692577307273E07329961
chr187723764677237707E074-39257
chr187723796377238046E074-38918
chr187725653577258114E074-18850
chr187726599577266077E074-10887
chr187726618277266328E074-10636
chr187726848977268688E074-8276
chr187728015377280704E0743189
chr187728568277285749E0748718
chr187728845277288609E07411488
chr187728869077289539E07411726
chr187729993877299988E07422974
chr187730012177300175E07423157
chr187730036577300415E07423401
chr187730054277300928E07423578
chr187730096977301019E07424005
chr187730121977301259E07424255
chr187730137477301490E07424410
chr187730282577302906E07425861
chr187730323877303311E07426274
chr187730341177303679E07426447
chr187730368277303739E07426718
chr187730386277303912E07426898
chr187730413277304340E07427168
chr187730499577305045E07428031
chr187730542277305472E07428458
chr187730573177306185E07428767
chr187730743577307597E07430471
chr187730765377307703E07430689
chr187730780477307854E07430840
chr187730788877307930E07430924
chr187732040577320458E07443441
chr187732058277320632E07443618
chr187722742877227494E081-49470
chr187722754377227715E081-49249
chr187722798977228099E081-48865
chr187722824877228414E081-48550
chr187722850077228712E081-48252
chr187722905177229121E081-47843
chr187722964277229729E081-47235
chr187722990177229959E081-47005
chr187722999277230077E081-46887
chr187723011477230357E081-46607
chr187723040277230560E081-46404
chr187723062877230761E081-46203
chr187723151177231621E081-45343
chr187725362877253791E081-23173
chr187725534377255403E081-21561
chr187725579677255881E081-21083
chr187725596877256077E081-20887
chr187725615577256446E081-20518
chr187725653577258114E081-18850
chr187726848977268688E081-8276
chr187727979277280124E0812828
chr187728015377280704E0813189
chr187728568277285749E0818718
chr187728575377285951E0818789
chr187728596577286440E0819001
chr187728753677287646E08110572
chr187728765677287722E08110692
chr187728777377287908E08110809
chr187728801377288148E08111049
chr187728819177288288E08111227
chr187728845277288609E08111488
chr187728869077289539E08111726
chr187730491577304980E08127951
chr187730692577307273E08129961
chr187730743577307597E08130471
chr187730765377307703E08130689
chr187730780477307854E08130840
chr187730788877307930E08130924
chr187732657777326799E08149613
chr187722824877228414E082-48550
chr187722850077228712E082-48252
chr187723062877230761E082-46203
chr187725534377255403E082-21561
chr187726618277266328E082-10636