rs12925472

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

ZCCHC14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0147 (4418/29910,GnomAD)
T=0134 (3912/29118,TOPMED)
T=0218 (1092/5008,1000G)
T=0121 (465/3854,ALSPAC)
T=0119 (443/3708,TWINSUK)

Position: chr16:87447426 (GRCh38.p7) (16q24.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 340 Enhancers around

Promoter: 44 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 16	NC_000016.10:g.87447426C>T
GRCh37.p13 chr 16	NC_000016.9:g.87481032C>T

Gene: ZCCHC14, zinc finger CCHC-type containing 14(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZCCHC14 transcript	NM_015144.2:c.	N/A	Intron Variant
ZCCHC14 transcript variant X1	XM_005255858.3:c.	N/A	Intron Variant
ZCCHC14 transcript variant X4	XM_011522964.2:c.	N/A	Intron Variant
ZCCHC14 transcript variant X3	XM_017023082.1:c.	N/A	Intron Variant
ZCCHC14 transcript variant X2	XR_243401.3:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.890	T=0.110
1000Genomes	American	Sub	694	C=0.670	T=0.330
1000Genomes	East Asian	Sub	1008	C=0.554	T=0.446
1000Genomes	Europe	Sub	1006	C=0.870	T=0.130
1000Genomes	Global	Study-wide	5008	C=0.782	T=0.218
1000Genomes	South Asian	Sub	978	C=0.860	T=0.140
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.879	T=0.121
The Genome Aggregation Database	African	Sub	8714	C=0.885	T=0.115
The Genome Aggregation Database	American	Sub	836	C=0.650	T=0.350
The Genome Aggregation Database	East Asian	Sub	1604	C=0.550	T=0.450
The Genome Aggregation Database	Europe	Sub	18454	C=0.872	T=0.127
The Genome Aggregation Database	Global	Study-wide	29910	C=0.852	T=0.147
The Genome Aggregation Database	Other	Sub	302	C=0.850	T=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.865	T=0.134
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.881	T=0.119

PMID	Title	Author	Journal
22377092	ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.	Wang KS	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs12925472	0.00025	nicotine dependence (smoking)	22377092

eQTL of rs12925472 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 rs12925472 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 )
chr16	87468266	87468306	E067	-12726
chr16	87468827	87468877	E067	-12155
chr16	87468933	87470319	E067	-10713
chr16	87470375	87470601	E067	-10431
chr16	87494647	87494702	E067	13615
chr16	87494728	87494891	E067	13696
chr16	87494927	87495666	E067	13895
chr16	87496707	87496808	E067	15675
chr16	87496885	87496935	E067	15853
chr16	87497015	87497069	E067	15983
chr16	87497357	87499382	E067	16325
chr16	87499503	87499877	E067	18471
chr16	87499913	87500113	E067	18881
chr16	87500224	87500472	E067	19192
chr16	87500504	87500620	E067	19472
chr16	87503405	87503556	E067	22373
chr16	87503940	87504017	E067	22908
chr16	87504028	87504110	E067	22996
chr16	87504114	87504232	E067	23082
chr16	87504294	87504388	E067	23262
chr16	87504855	87505216	E067	23823
chr16	87505233	87505591	E067	24201
chr16	87505701	87505786	E067	24669
chr16	87505965	87506043	E067	24933
chr16	87509312	87509634	E067	28280
chr16	87509648	87509725	E067	28616
chr16	87509735	87509872	E067	28703
chr16	87510929	87511529	E067	29897
chr16	87514546	87514606	E067	33514
chr16	87514649	87514699	E067	33617
chr16	87518629	87518708	E067	37597
chr16	87519327	87519367	E067	38295
chr16	87519424	87519590	E067	38392
chr16	87519645	87519742	E067	38613
chr16	87519790	87519831	E067	38758
chr16	87519959	87520035	E067	38927
chr16	87520047	87520148	E067	39015
chr16	87520334	87520459	E067	39302
chr16	87520489	87520775	E067	39457
chr16	87457706	87457756	E068	-23276
chr16	87458001	87458072	E068	-22960
chr16	87458074	87458218	E068	-22814
chr16	87458225	87458357	E068	-22675
chr16	87458387	87458437	E068	-22595
chr16	87458460	87458511	E068	-22521
chr16	87468827	87468877	E068	-12155
chr16	87468933	87470319	E068	-10713
chr16	87470375	87470601	E068	-10431
chr16	87494927	87495666	E068	13895
chr16	87497357	87499382	E068	16325
chr16	87499503	87499877	E068	18471
chr16	87499913	87500113	E068	18881
chr16	87502280	87502410	E068	21248
chr16	87502481	87502597	E068	21449
chr16	87502851	87502999	E068	21819
chr16	87503405	87503556	E068	22373
chr16	87504855	87505216	E068	23823
chr16	87505233	87505591	E068	24201
chr16	87505701	87505786	E068	24669
chr16	87505965	87506043	E068	24933
chr16	87506230	87506290	E068	25198
chr16	87509312	87509634	E068	28280
chr16	87509648	87509725	E068	28616
chr16	87509735	87509872	E068	28703
chr16	87510394	87510476	E068	29362
chr16	87510669	87510752	E068	29637
chr16	87510847	87510902	E068	29815
chr16	87510929	87511529	E068	29897
chr16	87511809	87511880	E068	30777
chr16	87514546	87514606	E068	33514
chr16	87514649	87514699	E068	33617
chr16	87514778	87514822	E068	33746
chr16	87517959	87518365	E068	36927
chr16	87518370	87518589	E068	37338
chr16	87518629	87518708	E068	37597
chr16	87518730	87518848	E068	37698
chr16	87519327	87519367	E068	38295
chr16	87519424	87519590	E068	38392
chr16	87519645	87519742	E068	38613
chr16	87519790	87519831	E068	38758
chr16	87519959	87520035	E068	38927
chr16	87520047	87520148	E068	39015
chr16	87520334	87520459	E068	39302
chr16	87521726	87521803	E068	40694
chr16	87521934	87521997	E068	40902
chr16	87522037	87522097	E068	41005
chr16	87458001	87458072	E069	-22960
chr16	87458074	87458218	E069	-22814
chr16	87458225	87458357	E069	-22675
chr16	87458387	87458437	E069	-22595
chr16	87460495	87460644	E069	-20388
chr16	87460656	87460759	E069	-20273
chr16	87460849	87461000	E069	-20032
chr16	87467380	87467445	E069	-13587
chr16	87468827	87468877	E069	-12155
chr16	87468933	87470319	E069	-10713
chr16	87470375	87470601	E069	-10431
chr16	87497357	87499382	E069	16325
chr16	87499503	87499877	E069	18471
chr16	87499913	87500113	E069	18881
chr16	87500224	87500472	E069	19192
chr16	87502851	87502999	E069	21819
chr16	87503405	87503556	E069	22373
chr16	87509312	87509634	E069	28280
chr16	87509648	87509725	E069	28616
chr16	87509735	87509872	E069	28703
chr16	87510929	87511529	E069	29897
chr16	87519424	87519590	E069	38392
chr16	87519645	87519742	E069	38613
chr16	87519790	87519831	E069	38758
chr16	87519959	87520035	E069	38927
chr16	87520047	87520148	E069	39015
chr16	87520334	87520459	E069	39302
chr16	87520489	87520775	E069	39457
chr16	87510847	87510902	E070	29815
chr16	87510929	87511529	E070	29897
chr16	87519959	87520035	E070	38927
chr16	87520047	87520148	E070	39015
chr16	87520334	87520459	E070	39302
chr16	87520489	87520775	E070	39457
chr16	87521934	87521997	E070	40902
chr16	87522426	87522486	E070	41394
chr16	87522612	87522874	E070	41580
chr16	87527621	87527759	E070	46589
chr16	87468266	87468306	E071	-12726
chr16	87468827	87468877	E071	-12155
chr16	87468933	87470319	E071	-10713
chr16	87470375	87470601	E071	-10431
chr16	87471042	87471118	E071	-9914
chr16	87494728	87494891	E071	13696
chr16	87494927	87495666	E071	13895
chr16	87497357	87499382	E071	16325
chr16	87499503	87499877	E071	18471
chr16	87499913	87500113	E071	18881
chr16	87500224	87500472	E071	19192
chr16	87502280	87502410	E071	21248
chr16	87502481	87502597	E071	21449
chr16	87502851	87502999	E071	21819
chr16	87503405	87503556	E071	22373
chr16	87503940	87504017	E071	22908
chr16	87504028	87504110	E071	22996
chr16	87504114	87504232	E071	23082
chr16	87504294	87504388	E071	23262
chr16	87504657	87504701	E071	23625
chr16	87504855	87505216	E071	23823
chr16	87505233	87505591	E071	24201
chr16	87505701	87505786	E071	24669
chr16	87505965	87506043	E071	24933
chr16	87508425	87508831	E071	27393
chr16	87509312	87509634	E071	28280
chr16	87509648	87509725	E071	28616
chr16	87509735	87509872	E071	28703
chr16	87510394	87510476	E071	29362
chr16	87510669	87510752	E071	29637
chr16	87510847	87510902	E071	29815
chr16	87514546	87514606	E071	33514
chr16	87514649	87514699	E071	33617
chr16	87514778	87514822	E071	33746
chr16	87514909	87514982	E071	33877
chr16	87517959	87518365	E071	36927
chr16	87518370	87518589	E071	37338
chr16	87519424	87519590	E071	38392
chr16	87519645	87519742	E071	38613
chr16	87519790	87519831	E071	38758
chr16	87519959	87520035	E071	38927
chr16	87520047	87520148	E071	39015
chr16	87520334	87520459	E071	39302
chr16	87520489	87520775	E071	39457
chr16	87521726	87521803	E071	40694
chr16	87521934	87521997	E071	40902
chr16	87522037	87522097	E071	41005
chr16	87522269	87522309	E071	41237
chr16	87522426	87522486	E071	41394
chr16	87522612	87522874	E071	41580
chr16	87446000	87446054	E072	-34978
chr16	87446106	87446165	E072	-34867
chr16	87446371	87446443	E072	-34589
chr16	87468266	87468306	E072	-12726
chr16	87468827	87468877	E072	-12155
chr16	87468933	87470319	E072	-10713
chr16	87494647	87494702	E072	13615
chr16	87494728	87494891	E072	13696
chr16	87494927	87495666	E072	13895
chr16	87497357	87499382	E072	16325
chr16	87499503	87499877	E072	18471
chr16	87499913	87500113	E072	18881
chr16	87500224	87500472	E072	19192
chr16	87500504	87500620	E072	19472
chr16	87500832	87501102	E072	19800
chr16	87501125	87501169	E072	20093
chr16	87502851	87502999	E072	21819
chr16	87503405	87503556	E072	22373
chr16	87503940	87504017	E072	22908
chr16	87504028	87504110	E072	22996
chr16	87509312	87509634	E072	28280
chr16	87509648	87509725	E072	28616
chr16	87509735	87509872	E072	28703
chr16	87510394	87510476	E072	29362
chr16	87510669	87510752	E072	29637
chr16	87510847	87510902	E072	29815
chr16	87510929	87511529	E072	29897
chr16	87514546	87514606	E072	33514
chr16	87514649	87514699	E072	33617
chr16	87514778	87514822	E072	33746
chr16	87519645	87519742	E072	38613
chr16	87519790	87519831	E072	38758
chr16	87519959	87520035	E072	38927
chr16	87520047	87520148	E072	39015
chr16	87520334	87520459	E072	39302
chr16	87520489	87520775	E072	39457
chr16	87445064	87445204	E073	-35828
chr16	87445316	87445366	E073	-35666
chr16	87445699	87445755	E073	-35277
chr16	87445797	87445855	E073	-35177
chr16	87446000	87446054	E073	-34978
chr16	87446106	87446165	E073	-34867
chr16	87458001	87458072	E073	-22960
chr16	87458074	87458218	E073	-22814
chr16	87458225	87458357	E073	-22675
chr16	87458387	87458437	E073	-22595
chr16	87458460	87458511	E073	-22521
chr16	87458776	87458826	E073	-22206
chr16	87460194	87460331	E073	-20701
chr16	87465154	87466019	E073	-15013
chr16	87466122	87466210	E073	-14822
chr16	87468266	87468306	E073	-12726
chr16	87468827	87468877	E073	-12155
chr16	87468933	87470319	E073	-10713
chr16	87470375	87470601	E073	-10431
chr16	87494647	87494702	E073	13615
chr16	87494728	87494891	E073	13696
chr16	87494927	87495666	E073	13895
chr16	87496707	87496808	E073	15675
chr16	87496885	87496935	E073	15853
chr16	87497015	87497069	E073	15983
chr16	87497357	87499382	E073	16325
chr16	87499503	87499877	E073	18471
chr16	87499913	87500113	E073	18881
chr16	87500224	87500472	E073	19192
chr16	87500504	87500620	E073	19472
chr16	87502280	87502410	E073	21248
chr16	87502481	87502597	E073	21449
chr16	87502851	87502999	E073	21819
chr16	87503405	87503556	E073	22373
chr16	87503940	87504017	E073	22908
chr16	87504028	87504110	E073	22996
chr16	87504114	87504232	E073	23082
chr16	87505233	87505591	E073	24201
chr16	87509312	87509634	E073	28280
chr16	87509648	87509725	E073	28616
chr16	87509735	87509872	E073	28703
chr16	87510394	87510476	E073	29362
chr16	87510669	87510752	E073	29637
chr16	87510847	87510902	E073	29815
chr16	87510929	87511529	E073	29897
chr16	87517844	87517898	E073	36812
chr16	87517959	87518365	E073	36927
chr16	87518370	87518589	E073	37338
chr16	87518629	87518708	E073	37597
chr16	87518730	87518848	E073	37698
chr16	87519327	87519367	E073	38295
chr16	87519424	87519590	E073	38392
chr16	87519645	87519742	E073	38613
chr16	87519790	87519831	E073	38758
chr16	87519959	87520035	E073	38927
chr16	87521726	87521803	E073	40694
chr16	87521934	87521997	E073	40902
chr16	87522037	87522097	E073	41005
chr16	87522269	87522309	E073	41237
chr16	87522426	87522486	E073	41394
chr16	87522612	87522874	E073	41580
chr16	87468827	87468877	E074	-12155
chr16	87468933	87470319	E074	-10713
chr16	87470375	87470601	E074	-10431
chr16	87497357	87499382	E074	16325
chr16	87499503	87499877	E074	18471
chr16	87499913	87500113	E074	18881
chr16	87500224	87500472	E074	19192
chr16	87500504	87500620	E074	19472
chr16	87509312	87509634	E074	28280
chr16	87509648	87509725	E074	28616
chr16	87509735	87509872	E074	28703
chr16	87510394	87510476	E074	29362
chr16	87510669	87510752	E074	29637
chr16	87510847	87510902	E074	29815
chr16	87510929	87511529	E074	29897
chr16	87517959	87518365	E074	36927
chr16	87518370	87518589	E074	37338
chr16	87519424	87519590	E074	38392
chr16	87519645	87519742	E074	38613
chr16	87519790	87519831	E074	38758
chr16	87519959	87520035	E074	38927
chr16	87520047	87520148	E074	39015
chr16	87520334	87520459	E074	39302
chr16	87520489	87520775	E074	39457
chr16	87521726	87521803	E074	40694
chr16	87521934	87521997	E074	40902
chr16	87522037	87522097	E074	41005
chr16	87522269	87522309	E074	41237
chr16	87522426	87522486	E074	41394
chr16	87522612	87522874	E074	41580
chr16	87488365	87488415	E081	7333
chr16	87488467	87488511	E081	7435
chr16	87488990	87489040	E081	7958
chr16	87509312	87509634	E081	28280
chr16	87509648	87509725	E081	28616
chr16	87509735	87509872	E081	28703
chr16	87510394	87510476	E081	29362
chr16	87510669	87510752	E081	29637
chr16	87510847	87510902	E081	29815
chr16	87510929	87511529	E081	29897
chr16	87515818	87516128	E081	34786
chr16	87516744	87516784	E081	35712
chr16	87517197	87517475	E081	36165
chr16	87517673	87517723	E081	36641
chr16	87517844	87517898	E081	36812
chr16	87517959	87518365	E081	36927
chr16	87518370	87518589	E081	37338
chr16	87518629	87518708	E081	37597
chr16	87518730	87518848	E081	37698
chr16	87519327	87519367	E081	38295
chr16	87519424	87519590	E081	38392
chr16	87519645	87519742	E081	38613
chr16	87519790	87519831	E081	38758
chr16	87519959	87520035	E081	38927
chr16	87520047	87520148	E081	39015
chr16	87520334	87520459	E081	39302
chr16	87520489	87520775	E081	39457
chr16	87521726	87521803	E081	40694
chr16	87521934	87521997	E081	40902
chr16	87522037	87522097	E081	41005
chr16	87522269	87522309	E081	41237
chr16	87522426	87522486	E081	41394
chr16	87522612	87522874	E081	41580
chr16	87527621	87527759	E081	46589
chr16	87489373	87489868	E082	8341
chr16	87519645	87519742	E082	38613
chr16	87519790	87519831	E082	38758
chr16	87519959	87520035	E082	38927
chr16	87520047	87520148	E082	39015

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr16	87523945	87524785	E067	42913
chr16	87525319	87525586	E067	44287
chr16	87525676	87525886	E067	44644
chr16	87526297	87527176	E067	45265
chr16	87523945	87524785	E068	42913
chr16	87525319	87525586	E068	44287
chr16	87525676	87525886	E068	44644
chr16	87523945	87524785	E069	42913
chr16	87525319	87525586	E069	44287
chr16	87525676	87525886	E069	44644
chr16	87525972	87526113	E069	44940
chr16	87526115	87526170	E069	45083
chr16	87526171	87526248	E069	45139
chr16	87526297	87527176	E069	45265
chr16	87523945	87524785	E070	42913
chr16	87525319	87525586	E070	44287
chr16	87525676	87525886	E070	44644
chr16	87525972	87526113	E070	44940
chr16	87526115	87526170	E070	45083
chr16	87526171	87526248	E070	45139
chr16	87526297	87527176	E070	45265
chr16	87523945	87524785	E071	42913
chr16	87525319	87525586	E071	44287
chr16	87525676	87525886	E071	44644
chr16	87523945	87524785	E072	42913
chr16	87525319	87525586	E072	44287
chr16	87525676	87525886	E072	44644
chr16	87525972	87526113	E072	44940
chr16	87526115	87526170	E072	45083
chr16	87526171	87526248	E072	45139
chr16	87526297	87527176	E072	45265
chr16	87523945	87524785	E073	42913
chr16	87525319	87525586	E073	44287
chr16	87525676	87525886	E073	44644
chr16	87523945	87524785	E074	42913
chr16	87525319	87525586	E074	44287
chr16	87525676	87525886	E074	44644
chr16	87523945	87524785	E082	42913
chr16	87525319	87525586	E082	44287
chr16	87525676	87525886	E082	44644
chr16	87525972	87526113	E082	44940
chr16	87526115	87526170	E082	45083
chr16	87526171	87526248	E082	45139
chr16	87526297	87527176	E082	45265