rs4898519

Organism: Homo sapiens

Alleles: A>G / A>T

Gene : Feature

TROAP : 2KB Upstream Variant
LOC101927267 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0292 (8760/29952,GnomAD)
G=0345 (10053/29118,TOPMED)
G=0260 (1302/5008,1000G)
G=0159 (611/3854,ALSPAC)
G=0145 (539/3708,TWINSUK)

Position: chr12:49320320 (GRCh38.p7) (12q13.12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 230 Enhancers around

Promoter: 38 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.49320320A>G
GRCh38.p7 chr 12	NC_000012.12:g.49320320A>T
GRCh37.p13 chr 12	NC_000012.11:g.49714103A>G
GRCh37.p13 chr 12	NC_000012.11:g.49714103A>T

Gene: TROAP, trophinin associated protein(plus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
TROAP transcript variant 2	NM_001100620.1:c.	N/A	N/A
TROAP transcript variant 3	NM_001278324.1:c.	N/A	N/A
TROAP transcript variant 1	NM_005480.3:c.	N/A	N/A
TROAP transcript variant X6	XM_011537725.2:c.	N/A	Upstream Transcript Variant
TROAP transcript variant X1	XM_006719181.1:c.	N/A	N/A
TROAP transcript variant X2	XM_011537723.1:c.	N/A	N/A
TROAP transcript variant X4	XM_011537724.1:c.	N/A	N/A
TROAP transcript variant X3	XR_944445.1:n.	N/A	N/A
TROAP transcript variant X5	XR_944446.1:n.	N/A	N/A

Gene: LOC101927267, uncharacterized LOC101927267(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101927267 transcript	NR_120449.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.358	G=0.642
1000Genomes	American	Sub	694	A=0.860	G=0.140
1000Genomes	East Asian	Sub	1008	A=0.959	G=0.041
1000Genomes	Europe	Sub	1006	A=0.838	G=0.162
1000Genomes	Global	Study-wide	5008	A=0.740	G=0.260
1000Genomes	South Asian	Sub	978	A=0.840	G=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.841	G=0.159
The Genome Aggregation Database	African	Sub	8706	A=0.439	G=0.561
The Genome Aggregation Database	American	Sub	838	A=0.860	G=0.140
The Genome Aggregation Database	East Asian	Sub	1620	A=0.945	G=0.055
The Genome Aggregation Database	Europe	Sub	18486	A=0.803	G=0.196
The Genome Aggregation Database	Global	Study-wide	29952	A=0.707	G=0.292
The Genome Aggregation Database	Other	Sub	302	A=0.860	G=0.140
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.654	G=0.345
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.855	G=0.145

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs4898519	0.00087	alcohol dependence	20201924

eQTL of rs4898519 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 rs4898519 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	113502125	113502208	E067	13991
chr12	113502344	113502431	E067	14210
chr12	113502786	113502836	E067	14652
chr12	113504698	113505049	E067	16564
chr12	113505191	113505561	E067	17057
chr12	113509645	113509831	E067	21511
chr12	113509899	113510202	E067	21765
chr12	113528374	113528458	E067	40240
chr12	113528484	113528582	E067	40350
chr12	113528593	113528804	E067	40459
chr12	113528913	113529079	E067	40779
chr12	113529129	113529207	E067	40995
chr12	113529259	113529357	E067	41125
chr12	113529373	113529427	E067	41239
chr12	113529476	113529562	E067	41342
chr12	113535019	113535121	E067	46885
chr12	113535133	113535187	E067	46999
chr12	113535245	113535303	E067	47111
chr12	113535378	113536625	E067	47244
chr12	113536667	113536763	E067	48533
chr12	113478394	113479076	E068	-9058
chr12	113493390	113493888	E068	5256
chr12	113502344	113502431	E068	14210
chr12	113502786	113502836	E068	14652
chr12	113502940	113503003	E068	14806
chr12	113503004	113503478	E068	14870
chr12	113504482	113504536	E068	16348
chr12	113504698	113505049	E068	16564
chr12	113508552	113508611	E068	20418
chr12	113508659	113509611	E068	20525
chr12	113509645	113509831	E068	21511
chr12	113509899	113510202	E068	21765
chr12	113510224	113510317	E068	22090
chr12	113510431	113510484	E068	22297
chr12	113510860	113510916	E068	22726
chr12	113510960	113511037	E068	22826
chr12	113511594	113511739	E068	23460
chr12	113512040	113512131	E068	23906
chr12	113512137	113512217	E068	24003
chr12	113512298	113512352	E068	24164
chr12	113512359	113512526	E068	24225
chr12	113512551	113512601	E068	24417
chr12	113512649	113512713	E068	24515
chr12	113512785	113513797	E068	24651
chr12	113528484	113528582	E068	40350
chr12	113529129	113529207	E068	40995
chr12	113529259	113529357	E068	41125
chr12	113529373	113529427	E068	41239
chr12	113529476	113529562	E068	41342
chr12	113535019	113535121	E068	46885
chr12	113535133	113535187	E068	46999
chr12	113535245	113535303	E068	47111
chr12	113536667	113536763	E068	48533
chr12	113496147	113496238	E069	8013
chr12	113496323	113496373	E069	8189
chr12	113496485	113496653	E069	8351
chr12	113496727	113496800	E069	8593
chr12	113496866	113497435	E069	8732
chr12	113497488	113497548	E069	9354
chr12	113497578	113497749	E069	9444
chr12	113497847	113497922	E069	9713
chr12	113497925	113497979	E069	9791
chr12	113498003	113498088	E069	9869
chr12	113498104	113498154	E069	9970
chr12	113498224	113498274	E069	10090
chr12	113498426	113498637	E069	10292
chr12	113498697	113498808	E069	10563
chr12	113498912	113498969	E069	10778
chr12	113498974	113499082	E069	10840
chr12	113500295	113500948	E069	12161
chr12	113501004	113501054	E069	12870
chr12	113501629	113501732	E069	13495
chr12	113502125	113502208	E069	13991
chr12	113502344	113502431	E069	14210
chr12	113504482	113504536	E069	16348
chr12	113504698	113505049	E069	16564
chr12	113507469	113507537	E069	19335
chr12	113507603	113508529	E069	19469
chr12	113508552	113508611	E069	20418
chr12	113509899	113510202	E069	21765
chr12	113510224	113510317	E069	22090
chr12	113510431	113510484	E069	22297
chr12	113512785	113513797	E069	24651
chr12	113534514	113534564	E069	46380
chr12	113534578	113534628	E069	46444
chr12	113534704	113534788	E069	46570
chr12	113534802	113534880	E069	46668
chr12	113534881	113534941	E069	46747
chr12	113535019	113535121	E069	46885
chr12	113535133	113535187	E069	46999
chr12	113535245	113535303	E069	47111
chr12	113535378	113536625	E069	47244
chr12	113536667	113536763	E069	48533
chr12	113498697	113498808	E070	10563
chr12	113498912	113498969	E070	10778
chr12	113498974	113499082	E070	10840
chr12	113499092	113499181	E070	10958
chr12	113500295	113500948	E070	12161
chr12	113501004	113501054	E070	12870
chr12	113501629	113501732	E070	13495
chr12	113502125	113502208	E070	13991
chr12	113502344	113502431	E070	14210
chr12	113502786	113502836	E070	14652
chr12	113502940	113503003	E070	14806
chr12	113503004	113503478	E070	14870
chr12	113504698	113505049	E070	16564
chr12	113507603	113508529	E070	19469
chr12	113508552	113508611	E070	20418
chr12	113508659	113509611	E070	20525
chr12	113509645	113509831	E070	21511
chr12	113535245	113535303	E070	47111
chr12	113536667	113536763	E070	48533
chr12	113496047	113496129	E071	7913
chr12	113496147	113496238	E071	8013
chr12	113508659	113509611	E071	20525
chr12	113509645	113509831	E071	21511
chr12	113509899	113510202	E071	21765
chr12	113534704	113534788	E071	46570
chr12	113534802	113534880	E071	46668
chr12	113534881	113534941	E071	46747
chr12	113535019	113535121	E071	46885
chr12	113535133	113535187	E071	46999
chr12	113535245	113535303	E071	47111
chr12	113535378	113536625	E071	47244
chr12	113536667	113536763	E071	48533
chr12	113493390	113493888	E072	5256
chr12	113496323	113496373	E072	8189
chr12	113496485	113496653	E072	8351
chr12	113496727	113496800	E072	8593
chr12	113498224	113498274	E072	10090
chr12	113498974	113499082	E072	10840
chr12	113499092	113499181	E072	10958
chr12	113499290	113499396	E072	11156
chr12	113500295	113500948	E072	12161
chr12	113501004	113501054	E072	12870
chr12	113534514	113534564	E072	46380
chr12	113534578	113534628	E072	46444
chr12	113534704	113534788	E072	46570
chr12	113534802	113534880	E072	46668
chr12	113534881	113534941	E072	46747
chr12	113535019	113535121	E072	46885
chr12	113535133	113535187	E072	46999
chr12	113468535	113468612	E073	-19522
chr12	113468658	113469098	E073	-19036
chr12	113493390	113493888	E073	5256
chr12	113496485	113496653	E073	8351
chr12	113496727	113496800	E073	8593
chr12	113496866	113497435	E073	8732
chr12	113500295	113500948	E073	12161
chr12	113501004	113501054	E073	12870
chr12	113501629	113501732	E073	13495
chr12	113502125	113502208	E073	13991
chr12	113502344	113502431	E073	14210
chr12	113504482	113504536	E073	16348
chr12	113504698	113505049	E073	16564
chr12	113505191	113505561	E073	17057
chr12	113509645	113509831	E073	21511
chr12	113509899	113510202	E073	21765
chr12	113510224	113510317	E073	22090
chr12	113512359	113512526	E073	24225
chr12	113512551	113512601	E073	24417
chr12	113512649	113512713	E073	24515
chr12	113512785	113513797	E073	24651
chr12	113528913	113529079	E073	40779
chr12	113529129	113529207	E073	40995
chr12	113529259	113529357	E073	41125
chr12	113529373	113529427	E073	41239
chr12	113529476	113529562	E073	41342
chr12	113534514	113534564	E073	46380
chr12	113534578	113534628	E073	46444
chr12	113534704	113534788	E073	46570
chr12	113534802	113534880	E073	46668
chr12	113534881	113534941	E073	46747
chr12	113535019	113535121	E073	46885
chr12	113535133	113535187	E073	46999
chr12	113535245	113535303	E073	47111
chr12	113535378	113536625	E073	47244
chr12	113536667	113536763	E073	48533
chr12	113536840	113536890	E073	48706
chr12	113500295	113500948	E074	12161
chr12	113501004	113501054	E074	12870
chr12	113502344	113502431	E074	14210
chr12	113507603	113508529	E074	19469
chr12	113508552	113508611	E074	20418
chr12	113508659	113509611	E074	20525
chr12	113509645	113509831	E074	21511
chr12	113509899	113510202	E074	21765
chr12	113512649	113512713	E074	24515
chr12	113529259	113529357	E074	41125
chr12	113534704	113534788	E074	46570
chr12	113534802	113534880	E074	46668
chr12	113534881	113534941	E074	46747
chr12	113535019	113535121	E074	46885
chr12	113535133	113535187	E074	46999
chr12	113535245	113535303	E074	47111
chr12	113535378	113536625	E074	47244
chr12	113536667	113536763	E074	48533
chr12	113468535	113468612	E081	-19522
chr12	113468658	113469098	E081	-19036
chr12	113493390	113493888	E081	5256
chr12	113496047	113496129	E081	7913
chr12	113496147	113496238	E081	8013
chr12	113496323	113496373	E081	8189
chr12	113496485	113496653	E081	8351
chr12	113496727	113496800	E081	8593
chr12	113497488	113497548	E081	9354
chr12	113497578	113497749	E081	9444
chr12	113500295	113500948	E081	12161
chr12	113502786	113502836	E081	14652
chr12	113502940	113503003	E081	14806
chr12	113503004	113503478	E081	14870
chr12	113503630	113503683	E081	15496
chr12	113503785	113503840	E081	15651
chr12	113514596	113514655	E081	26462
chr12	113514704	113514768	E081	26570
chr12	113528593	113528804	E081	40459
chr12	113528913	113529079	E081	40779
chr12	113529129	113529207	E081	40995
chr12	113529259	113529357	E081	41125
chr12	113529373	113529427	E081	41239
chr12	113529476	113529562	E081	41342
chr12	113535019	113535121	E081	46885
chr12	113535133	113535187	E081	46999
chr12	113535245	113535303	E081	47111
chr12	113535378	113536625	E081	47244
chr12	113496866	113497435	E082	8732
chr12	113502940	113503003	E082	14806
chr12	113503004	113503478	E082	14870
chr12	113535245	113535303	E082	47111
chr12	113535378	113536625	E082	47244

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	113494175	113494820	E067	6041
chr12	113494852	113495237	E067	6718
chr12	113495307	113495453	E067	7173
chr12	113495482	113495651	E067	7348
chr12	113494175	113494820	E068	6041
chr12	113494852	113495237	E068	6718
chr12	113495307	113495453	E068	7173
chr12	113495482	113495651	E068	7348
chr12	113494175	113494820	E069	6041
chr12	113494852	113495237	E069	6718
chr12	113495307	113495453	E069	7173
chr12	113495482	113495651	E069	7348
chr12	113494175	113494820	E070	6041
chr12	113494852	113495237	E070	6718
chr12	113495307	113495453	E070	7173
chr12	113495482	113495651	E070	7348
chr12	113494175	113494820	E071	6041
chr12	113494852	113495237	E071	6718
chr12	113495307	113495453	E071	7173
chr12	113495482	113495651	E071	7348
chr12	113494175	113494820	E072	6041
chr12	113494852	113495237	E072	6718
chr12	113495307	113495453	E072	7173
chr12	113495482	113495651	E072	7348
chr12	113494175	113494820	E073	6041
chr12	113494852	113495237	E073	6718
chr12	113495307	113495453	E073	7173
chr12	113495482	113495651	E073	7348
chr12	113494175	113494820	E074	6041
chr12	113494852	113495237	E074	6718
chr12	113495307	113495453	E074	7173
chr12	113495482	113495651	E074	7348
chr12	113495307	113495453	E081	7173
chr12	113495482	113495651	E081	7348
chr12	113494175	113494820	E082	6041
chr12	113494852	113495237	E082	6718
chr12	113495307	113495453	E082	7173
chr12	113495482	113495651	E082	7348