rs177820

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

NFATC1 : Intron Variant
LOC102723506 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

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)

Position: chr18:79516964 (GRCh38.p7) (18q23)

Phenotype: AD

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 262 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 18	NC_000018.10:g.79516964A>G
GRCh37.p13 chr 18	NC_000018.9:g.77276964A>G
NFATC1 RefSeqGene	NG_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 6	NM_001278669.1:c.	N/A	Intron Variant
NFATC1 transcript variant 7	NM_001278670.1:c.	N/A	Intron Variant
NFATC1 transcript variant 8	NM_001278672.1:c.	N/A	Intron Variant
NFATC1 transcript variant 10	NM_001278673.1:c.	N/A	Intron Variant
NFATC1 transcript variant 2	NM_006162.4:c.	N/A	Intron Variant
NFATC1 transcript variant 3	NM_172387.2:c.	N/A	Intron Variant
NFATC1 transcript variant 4	NM_172388.2:c.	N/A	Intron Variant
NFATC1 transcript variant 5	NM_172389.2:c.	N/A	Intron Variant
NFATC1 transcript variant 9	NM_001278675.1:c.	N/A	Genic Downstream Transcript Variant
NFATC1 transcript variant 1	NM_172390.2:c.	N/A	Genic Downstream Transcript Variant
NFATC1 transcript variant X1	XM_017025783.1:c.	N/A	Genic Downstream Transcript Variant

Gene: LOC102723506, uncharacterized LOC102723506(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102723506 transcript variant X1	XR_935689.1:n.768...XR_935689.1:n.7686T>C	T>C	Non Coding Transcript Variant
LOC102723506 transcript variant X2	XR_001753516.1:n....XR_001753516.1:n.6987T>C	T>C	Non Coding Transcript Variant
LOC102723506 transcript variant X3	XR_001753517.1:n....XR_001753517.1:n.7690T>C	T>C	Non Coding Transcript Variant
LOC102723506 transcript variant X4	XR_935690.2:n.691...XR_935690.2:n.6916T>C	T>C	Non Coding Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.663	G=0.337
1000Genomes	American	Sub	694	A=0.560	G=0.440
1000Genomes	East Asian	Sub	1008	A=0.276	G=0.724
1000Genomes	Europe	Sub	1006	A=0.644	G=0.356
1000Genomes	Global	Study-wide	5008	A=0.523	G=0.477
1000Genomes	South Asian	Sub	978	A=0.430	G=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.642	G=0.358
The Genome Aggregation Database	African	Sub	8720	A=0.650	G=0.350
The Genome Aggregation Database	American	Sub	838	A=0.520	G=0.480
The Genome Aggregation Database	East Asian	Sub	1610	A=0.278	G=0.722
The Genome Aggregation Database	Europe	Sub	18462	A=0.660	G=0.339
The Genome Aggregation Database	Global	Study-wide	29932	A=0.632	G=0.367
The Genome Aggregation Database	Other	Sub	302	A=0.600	G=0.400
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.623	G=0.376
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.629	G=0.371

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
19619005	Candidate gene analysis of femoral neck trabecular and cortical volumetric bone mineral density in older men.	Yerges LM	J Bone Miner Res
20357209	Molecular genetic studies of gene identification for osteoporosis: the 2009 update.	Xu XH	Endocr Rev
19453261	High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.	Yerges LM	J Bone Miner Res

SNP ID	p-value	Traits	Study
rs177820	0.000924	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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 )
chr18	77236722	77236913	E067	-40051
chr18	77236923	77237204	E067	-39760
chr18	77237206	77237575	E067	-39389
chr18	77237646	77237707	E067	-39257
chr18	77268489	77268688	E067	-8276
chr18	77279792	77280124	E067	2828
chr18	77280153	77280704	E067	3189
chr18	77285682	77285749	E067	8718
chr18	77285753	77285951	E067	8789
chr18	77285965	77286440	E067	9001
chr18	77286507	77287079	E067	9543
chr18	77292498	77292864	E067	15534
chr18	77292914	77293053	E067	15950
chr18	77299938	77299988	E067	22974
chr18	77300121	77300175	E067	23157
chr18	77300365	77300415	E067	23401
chr18	77300542	77300928	E067	23578
chr18	77300969	77301019	E067	24005
chr18	77301219	77301259	E067	24255
chr18	77301374	77301490	E067	24410
chr18	77302825	77302906	E067	25861
chr18	77256535	77258114	E068	-18850
chr18	77266182	77266328	E068	-10636
chr18	77280153	77280704	E068	3189
chr18	77285753	77285951	E068	8789
chr18	77285965	77286440	E068	9001
chr18	77286507	77287079	E068	9543
chr18	77288690	77289539	E068	11726
chr18	77299292	77299407	E068	22328
chr18	77299455	77299532	E068	22491
chr18	77299698	77299760	E068	22734
chr18	77299938	77299988	E068	22974
chr18	77300121	77300175	E068	23157
chr18	77300365	77300415	E068	23401
chr18	77300542	77300928	E068	23578
chr18	77300969	77301019	E068	24005
chr18	77301219	77301259	E068	24255
chr18	77301374	77301490	E068	24410
chr18	77303238	77303311	E068	26274
chr18	77303411	77303679	E068	26447
chr18	77303682	77303739	E068	26718
chr18	77303862	77303912	E068	26898
chr18	77307653	77307703	E068	30689
chr18	77307804	77307854	E068	30840
chr18	77307888	77307930	E068	30924
chr18	77308013	77308063	E068	31049
chr18	77308106	77308150	E068	31142
chr18	77236722	77236913	E069	-40051
chr18	77236923	77237204	E069	-39760
chr18	77237206	77237575	E069	-39389
chr18	77237646	77237707	E069	-39257
chr18	77251554	77252117	E069	-24847
chr18	77252150	77252328	E069	-24636
chr18	77256535	77258114	E069	-18850
chr18	77266182	77266328	E069	-10636
chr18	77288452	77288609	E069	11488
chr18	77288690	77289539	E069	11726
chr18	77292498	77292864	E069	15534
chr18	77292914	77293053	E069	15950
chr18	77299938	77299988	E069	22974
chr18	77300121	77300175	E069	23157
chr18	77300365	77300415	E069	23401
chr18	77300542	77300928	E069	23578
chr18	77300969	77301019	E069	24005
chr18	77301219	77301259	E069	24255
chr18	77301374	77301490	E069	24410
chr18	77302825	77302906	E069	25861
chr18	77303238	77303311	E069	26274
chr18	77303411	77303679	E069	26447
chr18	77303682	77303739	E069	26718
chr18	77303862	77303912	E069	26898
chr18	77304132	77304340	E069	27168
chr18	77304345	77304431	E069	27381
chr18	77307435	77307597	E069	30471
chr18	77307653	77307703	E069	30689
chr18	77307804	77307854	E069	30840
chr18	77307888	77307930	E069	30924
chr18	77308013	77308063	E069	31049
chr18	77308106	77308150	E069	31142
chr18	77320405	77320458	E069	43441
chr18	77320582	77320632	E069	43618
chr18	77320860	77320956	E069	43896
chr18	77227428	77227494	E070	-49470
chr18	77227543	77227715	E070	-49249
chr18	77228248	77228414	E070	-48550
chr18	77228500	77228712	E070	-48252
chr18	77229051	77229121	E070	-47843
chr18	77229642	77229729	E070	-47235
chr18	77229901	77229959	E070	-47005
chr18	77229992	77230077	E070	-46887
chr18	77230114	77230357	E070	-46607
chr18	77230402	77230560	E070	-46404
chr18	77230628	77230761	E070	-46203
chr18	77231511	77231621	E070	-45343
chr18	77231673	77232012	E070	-44952
chr18	77256535	77258114	E070	-18850
chr18	77262551	77262602	E070	-14362
chr18	77266182	77266328	E070	-10636
chr18	77268489	77268688	E070	-8276
chr18	77268897	77269028	E070	-7936
chr18	77269717	77269794	E070	-7170
chr18	77279792	77280124	E070	2828
chr18	77280153	77280704	E070	3189
chr18	77285753	77285951	E070	8789
chr18	77285965	77286440	E070	9001
chr18	77286507	77287079	E070	9543
chr18	77287118	77287250	E070	10154
chr18	77287273	77287345	E070	10309
chr18	77287401	77287455	E070	10437
chr18	77287536	77287646	E070	10572
chr18	77287656	77287722	E070	10692
chr18	77287773	77287908	E070	10809
chr18	77288013	77288148	E070	11049
chr18	77288191	77288288	E070	11227
chr18	77288452	77288609	E070	11488
chr18	77292498	77292864	E070	15534
chr18	77292914	77293053	E070	15950
chr18	77300542	77300928	E070	23578
chr18	77300969	77301019	E070	24005
chr18	77301219	77301259	E070	24255
chr18	77301374	77301490	E070	24410
chr18	77306787	77306896	E070	29823
chr18	77306925	77307273	E070	29961
chr18	77307435	77307597	E070	30471
chr18	77237206	77237575	E071	-39389
chr18	77237646	77237707	E071	-39257
chr18	77251554	77252117	E071	-24847
chr18	77256535	77258114	E071	-18850
chr18	77266182	77266328	E071	-10636
chr18	77268489	77268688	E071	-8276
chr18	77280153	77280704	E071	3189
chr18	77285682	77285749	E071	8718
chr18	77292498	77292864	E071	15534
chr18	77292914	77293053	E071	15950
chr18	77299292	77299407	E071	22328
chr18	77299455	77299532	E071	22491
chr18	77299698	77299760	E071	22734
chr18	77299938	77299988	E071	22974
chr18	77300121	77300175	E071	23157
chr18	77300365	77300415	E071	23401
chr18	77300542	77300928	E071	23578
chr18	77302825	77302906	E071	25861
chr18	77303238	77303311	E071	26274
chr18	77303411	77303679	E071	26447
chr18	77303682	77303739	E071	26718
chr18	77303862	77303912	E071	26898
chr18	77304132	77304340	E071	27168
chr18	77307435	77307597	E071	30471
chr18	77307653	77307703	E071	30689
chr18	77307804	77307854	E071	30840
chr18	77307888	77307930	E071	30924
chr18	77236722	77236913	E072	-40051
chr18	77236923	77237204	E072	-39760
chr18	77237206	77237575	E072	-39389
chr18	77237646	77237707	E072	-39257
chr18	77237963	77238046	E072	-38918
chr18	77251554	77252117	E072	-24847
chr18	77252150	77252328	E072	-24636
chr18	77255796	77255881	E072	-21083
chr18	77255968	77256077	E072	-20887
chr18	77256155	77256446	E072	-20518
chr18	77256535	77258114	E072	-18850
chr18	77266182	77266328	E072	-10636
chr18	77279792	77280124	E072	2828
chr18	77285682	77285749	E072	8718
chr18	77286507	77287079	E072	9543
chr18	77292914	77293053	E072	15950
chr18	77299698	77299760	E072	22734
chr18	77299938	77299988	E072	22974
chr18	77300121	77300175	E072	23157
chr18	77300365	77300415	E072	23401
chr18	77300542	77300928	E072	23578
chr18	77302825	77302906	E072	25861
chr18	77303238	77303311	E072	26274
chr18	77303411	77303679	E072	26447
chr18	77303682	77303739	E072	26718
chr18	77303862	77303912	E072	26898
chr18	77304132	77304340	E072	27168
chr18	77304345	77304431	E072	27381
chr18	77307435	77307597	E072	30471
chr18	77307653	77307703	E072	30689
chr18	77320405	77320458	E072	43441
chr18	77320582	77320632	E072	43618
chr18	77266182	77266328	E073	-10636
chr18	77285682	77285749	E073	8718
chr18	77306925	77307273	E073	29961
chr18	77237646	77237707	E074	-39257
chr18	77237963	77238046	E074	-38918
chr18	77256535	77258114	E074	-18850
chr18	77265995	77266077	E074	-10887
chr18	77266182	77266328	E074	-10636
chr18	77268489	77268688	E074	-8276
chr18	77280153	77280704	E074	3189
chr18	77285682	77285749	E074	8718
chr18	77288452	77288609	E074	11488
chr18	77288690	77289539	E074	11726
chr18	77299938	77299988	E074	22974
chr18	77300121	77300175	E074	23157
chr18	77300365	77300415	E074	23401
chr18	77300542	77300928	E074	23578
chr18	77300969	77301019	E074	24005
chr18	77301219	77301259	E074	24255
chr18	77301374	77301490	E074	24410
chr18	77302825	77302906	E074	25861
chr18	77303238	77303311	E074	26274
chr18	77303411	77303679	E074	26447
chr18	77303682	77303739	E074	26718
chr18	77303862	77303912	E074	26898
chr18	77304132	77304340	E074	27168
chr18	77304995	77305045	E074	28031
chr18	77305422	77305472	E074	28458
chr18	77305731	77306185	E074	28767
chr18	77307435	77307597	E074	30471
chr18	77307653	77307703	E074	30689
chr18	77307804	77307854	E074	30840
chr18	77307888	77307930	E074	30924
chr18	77320405	77320458	E074	43441
chr18	77320582	77320632	E074	43618
chr18	77227428	77227494	E081	-49470
chr18	77227543	77227715	E081	-49249
chr18	77227989	77228099	E081	-48865
chr18	77228248	77228414	E081	-48550
chr18	77228500	77228712	E081	-48252
chr18	77229051	77229121	E081	-47843
chr18	77229642	77229729	E081	-47235
chr18	77229901	77229959	E081	-47005
chr18	77229992	77230077	E081	-46887
chr18	77230114	77230357	E081	-46607
chr18	77230402	77230560	E081	-46404
chr18	77230628	77230761	E081	-46203
chr18	77231511	77231621	E081	-45343
chr18	77253628	77253791	E081	-23173
chr18	77255343	77255403	E081	-21561
chr18	77255796	77255881	E081	-21083
chr18	77255968	77256077	E081	-20887
chr18	77256155	77256446	E081	-20518
chr18	77256535	77258114	E081	-18850
chr18	77268489	77268688	E081	-8276
chr18	77279792	77280124	E081	2828
chr18	77280153	77280704	E081	3189
chr18	77285682	77285749	E081	8718
chr18	77285753	77285951	E081	8789
chr18	77285965	77286440	E081	9001
chr18	77287536	77287646	E081	10572
chr18	77287656	77287722	E081	10692
chr18	77287773	77287908	E081	10809
chr18	77288013	77288148	E081	11049
chr18	77288191	77288288	E081	11227
chr18	77288452	77288609	E081	11488
chr18	77288690	77289539	E081	11726
chr18	77304915	77304980	E081	27951
chr18	77306925	77307273	E081	29961
chr18	77307435	77307597	E081	30471
chr18	77307653	77307703	E081	30689
chr18	77307804	77307854	E081	30840
chr18	77307888	77307930	E081	30924
chr18	77326577	77326799	E081	49613
chr18	77228248	77228414	E082	-48550
chr18	77228500	77228712	E082	-48252
chr18	77230628	77230761	E082	-46203
chr18	77255343	77255403	E082	-21561
chr18	77266182	77266328	E082	-10636

rs177820

Genomic Coordinates

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

Gene: LOC102723506, uncharacterized LOC102723506(minus strand)

Population Frequency

P-Value

eQTL of rs177820 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs177820 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)