rs149212747

Organism: Homo sapiens

Alleles: dupC

Gene : Feature

LOC105369984 : Intron Variant

p-value: Check p-value

Variation Type: Indel (Insertion and Deletion)

Frequency:

dupC=0001 (30/29118,TOPMED)
dupC=0032 (158/5008,1000G)

Position: chr12:111398968-111398974 (GRCh38.p7) (12q24.12)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 260 Enhancers around

Promoter: 18 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.111398974dup
GRCh37.p13 chr 12	NC_000012.11:g.111836778dup

Gene: LOC105369984, uncharacterized LOC105369984(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC02356 transcript	XR_945342.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	(C)7=0.999	dupC=0.001
1000Genomes	American	Sub	694	(C)7=1.000	dupC=0.000
1000Genomes	East Asian	Sub	1008	(C)7=0.848	dupC=0.152
1000Genomes	Europe	Sub	1006	(C)7=1.000	dupC=0.000
1000Genomes	Global	Study-wide	5008	(C)7=0.968	dupC=0.032
1000Genomes	South Asian	Sub	978	(C)7=1.000	dupC=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	(C)7=0.999	dupC=0.001

PMID	Title	Author	Journal
29460428	Genomewide Association Study of Alcohol Dependence and Related Traits in a Thai Population.	Gelernter J	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs149212747	2.00E-12	alcohol consumption measurement	29460428
rs149212747	6.00E-10	alcohol dependence	29460428

eQTL of rs149212747 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 rs149212747 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 )
chr12	111846291	111846770	E067	9513
chr12	111846798	111848913	E067	10020
chr12	111849034	111849302	E067	12256
chr12	111849324	111849422	E067	12546
chr12	111849425	111849493	E067	12647
chr12	111849517	111849567	E067	12739
chr12	111849851	111850435	E067	13073
chr12	111850515	111851106	E067	13737
chr12	111851192	111852092	E067	14414
chr12	111865609	111865932	E067	28831
chr12	111865975	111866094	E067	29197
chr12	111866151	111866310	E067	29373
chr12	111871999	111873236	E067	35221
chr12	111873419	111874206	E067	36641
chr12	111874225	111875139	E067	37447
chr12	111875231	111875305	E067	38453
chr12	111875422	111876855	E067	38644
chr12	111883770	111885014	E067	46992
chr12	111846798	111848913	E068	10020
chr12	111849034	111849302	E068	12256
chr12	111849324	111849422	E068	12546
chr12	111849425	111849493	E068	12647
chr12	111849517	111849567	E068	12739
chr12	111849851	111850435	E068	13073
chr12	111850515	111851106	E068	13737
chr12	111851192	111852092	E068	14414
chr12	111862014	111862064	E068	25236
chr12	111862589	111862884	E068	25811
chr12	111862928	111863054	E068	26150
chr12	111863104	111863173	E068	26326
chr12	111863239	111863329	E068	26461
chr12	111863408	111863975	E068	26630
chr12	111863978	111864078	E068	27200
chr12	111866151	111866310	E068	29373
chr12	111866437	111866529	E068	29659
chr12	111866600	111867205	E068	29822
chr12	111867296	111867358	E068	30518
chr12	111867705	111869386	E068	30927
chr12	111871720	111871908	E068	34942
chr12	111871999	111873236	E068	35221
chr12	111873419	111874206	E068	36641
chr12	111874225	111875139	E068	37447
chr12	111875422	111876855	E068	38644
chr12	111877423	111877692	E068	40645
chr12	111877727	111877799	E068	40949
chr12	111877955	111878321	E068	41177
chr12	111882042	111883715	E068	45264
chr12	111883770	111885014	E068	46992
chr12	111886009	111886152	E068	49231
chr12	111804851	111805040	E069	-31738
chr12	111840716	111841651	E069	3938
chr12	111846291	111846770	E069	9513
chr12	111846798	111848913	E069	10020
chr12	111849034	111849302	E069	12256
chr12	111849324	111849422	E069	12546
chr12	111849425	111849493	E069	12647
chr12	111849517	111849567	E069	12739
chr12	111850515	111851106	E069	13737
chr12	111851192	111852092	E069	14414
chr12	111859763	111859871	E069	22985
chr12	111865609	111865932	E069	28831
chr12	111865975	111866094	E069	29197
chr12	111866151	111866310	E069	29373
chr12	111867705	111869386	E069	30927
chr12	111869406	111869921	E069	32628
chr12	111871612	111871667	E069	34834
chr12	111871720	111871908	E069	34942
chr12	111873419	111874206	E069	36641
chr12	111874225	111875139	E069	37447
chr12	111875422	111876855	E069	38644
chr12	111877727	111877799	E069	40949
chr12	111877955	111878321	E069	41177
chr12	111879614	111879764	E069	42836
chr12	111879930	111880046	E069	43152
chr12	111880076	111880154	E069	43298
chr12	111880195	111880418	E069	43417
chr12	111882042	111883715	E069	45264
chr12	111883770	111885014	E069	46992
chr12	111885193	111885339	E069	48415
chr12	111885392	111885485	E069	48614
chr12	111885532	111885679	E069	48754
chr12	111885685	111885795	E069	48907
chr12	111885830	111885884	E069	49052
chr12	111885892	111885969	E069	49114
chr12	111886009	111886152	E069	49231
chr12	111803877	111803927	E070	-32851
chr12	111803962	111804023	E070	-32755
chr12	111804082	111804167	E070	-32611
chr12	111804244	111804508	E070	-32270
chr12	111799421	111800426	E071	-36352
chr12	111804851	111805040	E071	-31738
chr12	111834577	111835549	E071	-1229
chr12	111846798	111848913	E071	10020
chr12	111849034	111849302	E071	12256
chr12	111849324	111849422	E071	12546
chr12	111849425	111849493	E071	12647
chr12	111849517	111849567	E071	12739
chr12	111849851	111850435	E071	13073
chr12	111850515	111851106	E071	13737
chr12	111851192	111852092	E071	14414
chr12	111852282	111852338	E071	15504
chr12	111852534	111852605	E071	15756
chr12	111852651	111852748	E071	15873
chr12	111852826	111853028	E071	16048
chr12	111853156	111853233	E071	16378
chr12	111862928	111863054	E071	26150
chr12	111863104	111863173	E071	26326
chr12	111863239	111863329	E071	26461
chr12	111863408	111863975	E071	26630
chr12	111863978	111864078	E071	27200
chr12	111865609	111865932	E071	28831
chr12	111865975	111866094	E071	29197
chr12	111866151	111866310	E071	29373
chr12	111866437	111866529	E071	29659
chr12	111867296	111867358	E071	30518
chr12	111867705	111869386	E071	30927
chr12	111869406	111869921	E071	32628
chr12	111871612	111871667	E071	34834
chr12	111871720	111871908	E071	34942
chr12	111871999	111873236	E071	35221
chr12	111873419	111874206	E071	36641
chr12	111874225	111875139	E071	37447
chr12	111875231	111875305	E071	38453
chr12	111875422	111876855	E071	38644
chr12	111877423	111877692	E071	40645
chr12	111877727	111877799	E071	40949
chr12	111877955	111878321	E071	41177
chr12	111878421	111878742	E071	41643
chr12	111878802	111878846	E071	42024
chr12	111879232	111879612	E071	42454
chr12	111879614	111879764	E071	42836
chr12	111879930	111880046	E071	43152
chr12	111880076	111880154	E071	43298
chr12	111880195	111880418	E071	43417
chr12	111880569	111881793	E071	43791
chr12	111882042	111883715	E071	45264
chr12	111883770	111885014	E071	46992
chr12	111885830	111885884	E071	49052
chr12	111885892	111885969	E071	49114
chr12	111886009	111886152	E071	49231
chr12	111799421	111800426	E072	-36352
chr12	111834577	111835549	E072	-1229
chr12	111846291	111846770	E072	9513
chr12	111846798	111848913	E072	10020
chr12	111849034	111849302	E072	12256
chr12	111849324	111849422	E072	12546
chr12	111849425	111849493	E072	12647
chr12	111849517	111849567	E072	12739
chr12	111849851	111850435	E072	13073
chr12	111850515	111851106	E072	13737
chr12	111851192	111852092	E072	14414
chr12	111863239	111863329	E072	26461
chr12	111863408	111863975	E072	26630
chr12	111863978	111864078	E072	27200
chr12	111864093	111864228	E072	27315
chr12	111865609	111865932	E072	28831
chr12	111865975	111866094	E072	29197
chr12	111866151	111866310	E072	29373
chr12	111866437	111866529	E072	29659
chr12	111866600	111867205	E072	29822
chr12	111867296	111867358	E072	30518
chr12	111867705	111869386	E072	30927
chr12	111871999	111873236	E072	35221
chr12	111873419	111874206	E072	36641
chr12	111874225	111875139	E072	37447
chr12	111875231	111875305	E072	38453
chr12	111875422	111876855	E072	38644
chr12	111877423	111877692	E072	40645
chr12	111877727	111877799	E072	40949
chr12	111877955	111878321	E072	41177
chr12	111878421	111878742	E072	41643
chr12	111879930	111880046	E072	43152
chr12	111880076	111880154	E072	43298
chr12	111880195	111880418	E072	43417
chr12	111880569	111881793	E072	43791
chr12	111882042	111883715	E072	45264
chr12	111883770	111885014	E072	46992
chr12	111885193	111885339	E072	48415
chr12	111885392	111885485	E072	48614
chr12	111885532	111885679	E072	48754
chr12	111885685	111885795	E072	48907
chr12	111885830	111885884	E072	49052
chr12	111885892	111885969	E072	49114
chr12	111886009	111886152	E072	49231
chr12	111834577	111835549	E073	-1229
chr12	111840716	111841651	E073	3938
chr12	111846798	111848913	E073	10020
chr12	111849034	111849302	E073	12256
chr12	111849324	111849422	E073	12546
chr12	111849425	111849493	E073	12647
chr12	111849517	111849567	E073	12739
chr12	111849851	111850435	E073	13073
chr12	111850515	111851106	E073	13737
chr12	111851192	111852092	E073	14414
chr12	111860798	111861023	E073	24020
chr12	111861095	111861156	E073	24317
chr12	111861436	111861556	E073	24658
chr12	111862014	111862064	E073	25236
chr12	111862103	111862228	E073	25325
chr12	111862390	111862494	E073	25612
chr12	111862589	111862884	E073	25811
chr12	111862928	111863054	E073	26150
chr12	111863104	111863173	E073	26326
chr12	111863239	111863329	E073	26461
chr12	111863408	111863975	E073	26630
chr12	111863978	111864078	E073	27200
chr12	111864093	111864228	E073	27315
chr12	111864229	111864876	E073	27451
chr12	111865609	111865932	E073	28831
chr12	111865975	111866094	E073	29197
chr12	111866151	111866310	E073	29373
chr12	111866437	111866529	E073	29659
chr12	111867705	111869386	E073	30927
chr12	111871612	111871667	E073	34834
chr12	111871720	111871908	E073	34942
chr12	111871999	111873236	E073	35221
chr12	111873419	111874206	E073	36641
chr12	111874225	111875139	E073	37447
chr12	111875231	111875305	E073	38453
chr12	111875422	111876855	E073	38644
chr12	111877423	111877692	E073	40645
chr12	111877727	111877799	E073	40949
chr12	111877955	111878321	E073	41177
chr12	111878421	111878742	E073	41643
chr12	111880569	111881793	E073	43791
chr12	111882042	111883715	E073	45264
chr12	111883770	111885014	E073	46992
chr12	111885193	111885339	E073	48415
chr12	111885392	111885485	E073	48614
chr12	111885532	111885679	E073	48754
chr12	111885685	111885795	E073	48907
chr12	111885830	111885884	E073	49052
chr12	111885892	111885969	E073	49114
chr12	111886009	111886152	E073	49231
chr12	111846291	111846770	E074	9513
chr12	111846798	111848913	E074	10020
chr12	111849034	111849302	E074	12256
chr12	111849324	111849422	E074	12546
chr12	111849425	111849493	E074	12647
chr12	111849517	111849567	E074	12739
chr12	111849851	111850435	E074	13073
chr12	111850515	111851106	E074	13737
chr12	111851192	111852092	E074	14414
chr12	111863239	111863329	E074	26461
chr12	111867705	111869386	E074	30927
chr12	111869406	111869921	E074	32628
chr12	111869936	111870005	E074	33158
chr12	111871612	111871667	E074	34834
chr12	111871720	111871908	E074	34942
chr12	111871999	111873236	E074	35221
chr12	111873419	111874206	E074	36641
chr12	111874225	111875139	E074	37447
chr12	111882042	111883715	E074	45264
chr12	111883770	111885014	E074	46992
chr12	111886009	111886152	E074	49231
chr12	111804851	111805040	E081	-31738
chr12	111803877	111803927	E082	-32851
chr12	111804851	111805040	E082	-31738
chr12	111877423	111877692	E082	40645
chr12	111877727	111877799	E082	40949

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	111805059	111807314	E067	-29464
chr12	111841768	111846238	E067	4990
chr12	111805059	111807314	E068	-29464
chr12	111841768	111846238	E068	4990
chr12	111805059	111807314	E069	-29464
chr12	111841768	111846238	E069	4990
chr12	111805059	111807314	E070	-29464
chr12	111805059	111807314	E071	-29464
chr12	111841768	111846238	E071	4990
chr12	111805059	111807314	E072	-29464
chr12	111841768	111846238	E072	4990
chr12	111805059	111807314	E073	-29464
chr12	111841768	111846238	E073	4990
chr12	111805059	111807314	E074	-29464
chr12	111841768	111846238	E074	4990
chr12	111805059	111807314	E081	-29464
chr12	111805059	111807314	E082	-29464
chr12	111841768	111846238	E082	4990