rs12222290

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

GALNT18 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0425 (12723/29900,GnomAD)
A==0444 (12950/29118,TOPMED)
A==0412 (2062/5008,1000G)
A==0375 (1446/3854,ALSPAC)
A==0366 (1356/3708,TWINSUK)

Position: chr11:11455298 (GRCh38.p7) (11p15.4)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 333 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.11455298A>G
GRCh37.p13 chr 11	NC_000011.9:g.11476845A>G

Gene: GALNT18, polypeptide N-acetylgalactosaminyltransferase 18(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GALNT18 transcript variant 1	NM_198516.2:c.	N/A	Intron Variant
GALNT18 transcript variant X1	XM_006718224.2:c.	N/A	Intron Variant
GALNT18 transcript variant X6	XM_006718225.2:c.	N/A	Intron Variant
GALNT18 transcript variant X3	XM_011520069.2:c.	N/A	Intron Variant
GALNT18 transcript variant X4	XM_011520070.2:c.	N/A	Intron Variant
GALNT18 transcript variant X5	XM_011520071.2:c.	N/A	Intron Variant
GALNT18 transcript variant X2	XM_011520068.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.645	G=0.355
1000Genomes	American	Sub	694	A=0.400	G=0.600
1000Genomes	East Asian	Sub	1008	A=0.170	G=0.830
1000Genomes	Europe	Sub	1006	A=0.381	G=0.619
1000Genomes	Global	Study-wide	5008	A=0.412	G=0.588
1000Genomes	South Asian	Sub	978	A=0.390	G=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.375	G=0.625
The Genome Aggregation Database	African	Sub	8684	A=0.587	G=0.413
The Genome Aggregation Database	American	Sub	836	A=0.390	G=0.610
The Genome Aggregation Database	East Asian	Sub	1622	A=0.152	G=0.848
The Genome Aggregation Database	Europe	Sub	18458	A=0.376	G=0.624
The Genome Aggregation Database	Global	Study-wide	29900	A=0.425	G=0.574
The Genome Aggregation Database	Other	Sub	300	A=0.360	G=0.640
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.444	G=0.555
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.366	G=0.634

PMID	Title	Author	Journal
29071344	Genetic Risk Variants Associated With Comorbid Alcohol Dependence and Major Depression.	Zhou H	JAMA Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs12222290	4E-06	alcohol dependence	29071344

eQTL of rs12222290 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 rs12222290 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 )
chr11	11428209	11428259	E067	-48586
chr11	11428345	11428461	E067	-48384
chr11	11428499	11429530	E067	-47315
chr11	11429589	11429655	E067	-47190
chr11	11431306	11431861	E067	-44984
chr11	11431909	11431978	E067	-44867
chr11	11432167	11432262	E067	-44583
chr11	11432302	11432400	E067	-44445
chr11	11441446	11441527	E067	-35318
chr11	11443188	11443295	E067	-33550
chr11	11443758	11443829	E067	-33016
chr11	11443896	11444662	E067	-32183
chr11	11444714	11444854	E067	-31991
chr11	11444858	11444958	E067	-31887
chr11	11444989	11445053	E067	-31792
chr11	11447201	11447251	E067	-29594
chr11	11447286	11447374	E067	-29471
chr11	11447430	11447766	E067	-29079
chr11	11447838	11448430	E067	-28415
chr11	11448627	11449448	E067	-27397
chr11	11449456	11449765	E067	-27080
chr11	11450172	11450222	E067	-26623
chr11	11450250	11450290	E067	-26555
chr11	11450395	11450445	E067	-26400
chr11	11450642	11450692	E067	-26153
chr11	11455142	11455208	E067	-21637
chr11	11455411	11455546	E067	-21299
chr11	11457484	11457611	E067	-19234
chr11	11457649	11457763	E067	-19082
chr11	11457901	11457996	E067	-18849
chr11	11458094	11458155	E067	-18690
chr11	11458172	11458319	E067	-18526
chr11	11458345	11458480	E067	-18365
chr11	11458483	11458764	E067	-18081
chr11	11464261	11464327	E067	-12518
chr11	11464340	11464641	E067	-12204
chr11	11464692	11464795	E067	-12050
chr11	11465814	11466693	E067	-10152
chr11	11468237	11468310	E067	-8535
chr11	11481980	11482290	E067	5135
chr11	11482494	11483657	E067	5649
chr11	11490604	11490849	E067	13759
chr11	11491106	11491217	E067	14261
chr11	11498123	11498372	E067	21278
chr11	11498650	11499154	E067	21805
chr11	11499439	11499675	E067	22594
chr11	11523334	11524675	E067	46489
chr11	11427907	11427961	E068	-48884
chr11	11428209	11428259	E068	-48586
chr11	11428345	11428461	E068	-48384
chr11	11428499	11429530	E068	-47315
chr11	11430095	11430901	E068	-45944
chr11	11430927	11431272	E068	-45573
chr11	11431306	11431861	E068	-44984
chr11	11432167	11432262	E068	-44583
chr11	11432302	11432400	E068	-44445
chr11	11436577	11436693	E068	-40152
chr11	11436724	11436814	E068	-40031
chr11	11437128	11437178	E068	-39667
chr11	11437307	11437523	E068	-39322
chr11	11437527	11437974	E068	-38871
chr11	11438117	11438842	E068	-38003
chr11	11443758	11443829	E068	-33016
chr11	11443896	11444662	E068	-32183
chr11	11444714	11444854	E068	-31991
chr11	11447430	11447766	E068	-29079
chr11	11447838	11448430	E068	-28415
chr11	11448627	11449448	E068	-27397
chr11	11449456	11449765	E068	-27080
chr11	11450172	11450222	E068	-26623
chr11	11451088	11451140	E068	-25705
chr11	11454923	11455046	E068	-21799
chr11	11455142	11455208	E068	-21637
chr11	11455411	11455546	E068	-21299
chr11	11458094	11458155	E068	-18690
chr11	11458172	11458319	E068	-18526
chr11	11458345	11458480	E068	-18365
chr11	11458483	11458764	E068	-18081
chr11	11465814	11466693	E068	-10152
chr11	11467046	11467398	E068	-9447
chr11	11467436	11467584	E068	-9261
chr11	11478345	11478403	E068	1500
chr11	11478456	11478537	E068	1611
chr11	11478596	11478680	E068	1751
chr11	11480769	11480899	E068	3924
chr11	11481070	11481120	E068	4225
chr11	11481281	11481394	E068	4436
chr11	11481980	11482290	E068	5135
chr11	11482494	11483657	E068	5649
chr11	11493646	11493723	E068	16801
chr11	11498650	11499154	E068	21805
chr11	11499439	11499675	E068	22594
chr11	11499728	11499866	E068	22883
chr11	11500016	11500091	E068	23171
chr11	11505270	11505369	E068	28425
chr11	11512819	11512904	E068	35974
chr11	11512905	11513005	E068	36060
chr11	11513186	11513329	E068	36341
chr11	11523093	11523327	E068	46248
chr11	11523334	11524675	E068	46489
chr11	11428345	11428461	E069	-48384
chr11	11428499	11429530	E069	-47315
chr11	11429589	11429655	E069	-47190
chr11	11430095	11430901	E069	-45944
chr11	11430927	11431272	E069	-45573
chr11	11431306	11431861	E069	-44984
chr11	11431909	11431978	E069	-44867
chr11	11441865	11441975	E069	-34870
chr11	11442020	11442404	E069	-34441
chr11	11447430	11447766	E069	-29079
chr11	11448627	11449448	E069	-27397
chr11	11449456	11449765	E069	-27080
chr11	11457154	11457469	E069	-19376
chr11	11457484	11457611	E069	-19234
chr11	11457649	11457763	E069	-19082
chr11	11457901	11457996	E069	-18849
chr11	11458094	11458155	E069	-18690
chr11	11458172	11458319	E069	-18526
chr11	11458345	11458480	E069	-18365
chr11	11458483	11458764	E069	-18081
chr11	11464261	11464327	E069	-12518
chr11	11465814	11466693	E069	-10152
chr11	11481281	11481394	E069	4436
chr11	11481980	11482290	E069	5135
chr11	11482494	11483657	E069	5649
chr11	11490604	11490849	E069	13759
chr11	11491106	11491217	E069	14261
chr11	11498650	11499154	E069	21805
chr11	11504184	11504234	E069	27339
chr11	11504409	11504535	E069	27564
chr11	11512819	11512904	E069	35974
chr11	11512905	11513005	E069	36060
chr11	11513186	11513329	E069	36341
chr11	11519833	11519957	E069	42988
chr11	11520044	11520094	E069	43199
chr11	11520382	11520561	E069	43537
chr11	11520793	11520872	E069	43948
chr11	11520940	11521060	E069	44095
chr11	11432412	11432526	E070	-44319
chr11	11441865	11441975	E070	-34870
chr11	11442020	11442404	E070	-34441
chr11	11442527	11442707	E070	-34138
chr11	11442812	11442862	E070	-33983
chr11	11443188	11443295	E070	-33550
chr11	11443758	11443829	E070	-33016
chr11	11443896	11444662	E070	-32183
chr11	11444714	11444854	E070	-31991
chr11	11448627	11449448	E070	-27397
chr11	11449456	11449765	E070	-27080
chr11	11465814	11466693	E070	-10152
chr11	11482494	11483657	E070	5649
chr11	11488897	11489069	E070	12052
chr11	11489078	11489154	E070	12233
chr11	11489169	11489225	E070	12324
chr11	11498650	11499154	E070	21805
chr11	11499439	11499675	E070	22594
chr11	11504184	11504234	E070	27339
chr11	11504409	11504535	E070	27564
chr11	11504759	11504964	E070	27914
chr11	11523334	11524675	E070	46489
chr11	11428345	11428461	E071	-48384
chr11	11428499	11429530	E071	-47315
chr11	11429589	11429655	E071	-47190
chr11	11430095	11430901	E071	-45944
chr11	11430927	11431272	E071	-45573
chr11	11431306	11431861	E071	-44984
chr11	11431909	11431978	E071	-44867
chr11	11436577	11436693	E071	-40152
chr11	11436724	11436814	E071	-40031
chr11	11437128	11437178	E071	-39667
chr11	11437307	11437523	E071	-39322
chr11	11437527	11437974	E071	-38871
chr11	11438117	11438842	E071	-38003
chr11	11442527	11442707	E071	-34138
chr11	11442812	11442862	E071	-33983
chr11	11443188	11443295	E071	-33550
chr11	11447430	11447766	E071	-29079
chr11	11447838	11448430	E071	-28415
chr11	11448627	11449448	E071	-27397
chr11	11449456	11449765	E071	-27080
chr11	11455142	11455208	E071	-21637
chr11	11455411	11455546	E071	-21299
chr11	11455630	11455818	E071	-21027
chr11	11455942	11455992	E071	-20853
chr11	11456075	11456128	E071	-20717
chr11	11458172	11458319	E071	-18526
chr11	11458345	11458480	E071	-18365
chr11	11458483	11458764	E071	-18081
chr11	11465814	11466693	E071	-10152
chr11	11479624	11479769	E071	2779
chr11	11481980	11482290	E071	5135
chr11	11482494	11483657	E071	5649
chr11	11484527	11484659	E071	7682
chr11	11498123	11498372	E071	21278
chr11	11498650	11499154	E071	21805
chr11	11499439	11499675	E071	22594
chr11	11499728	11499866	E071	22883
chr11	11504184	11504234	E071	27339
chr11	11504409	11504535	E071	27564
chr11	11504759	11504964	E071	27914
chr11	11505106	11505214	E071	28261
chr11	11505270	11505369	E071	28425
chr11	11428345	11428461	E072	-48384
chr11	11428499	11429530	E072	-47315
chr11	11430095	11430901	E072	-45944
chr11	11430927	11431272	E072	-45573
chr11	11431306	11431861	E072	-44984
chr11	11443758	11443829	E072	-33016
chr11	11447838	11448430	E072	-28415
chr11	11448627	11449448	E072	-27397
chr11	11449456	11449765	E072	-27080
chr11	11450642	11450692	E072	-26153
chr11	11454923	11455046	E072	-21799
chr11	11455142	11455208	E072	-21637
chr11	11455411	11455546	E072	-21299
chr11	11455630	11455818	E072	-21027
chr11	11455942	11455992	E072	-20853
chr11	11456075	11456128	E072	-20717
chr11	11457484	11457611	E072	-19234
chr11	11457649	11457763	E072	-19082
chr11	11457901	11457996	E072	-18849
chr11	11458094	11458155	E072	-18690
chr11	11458172	11458319	E072	-18526
chr11	11458345	11458480	E072	-18365
chr11	11464340	11464641	E072	-12204
chr11	11464692	11464795	E072	-12050
chr11	11465814	11466693	E072	-10152
chr11	11481980	11482290	E072	5135
chr11	11482494	11483657	E072	5649
chr11	11486233	11486313	E072	9388
chr11	11486652	11486741	E072	9807
chr11	11486744	11486794	E072	9899
chr11	11487010	11487072	E072	10165
chr11	11490604	11490849	E072	13759
chr11	11498650	11499154	E072	21805
chr11	11499439	11499675	E072	22594
chr11	11428345	11428461	E073	-48384
chr11	11428499	11429530	E073	-47315
chr11	11429589	11429655	E073	-47190
chr11	11429961	11430046	E073	-46799
chr11	11430095	11430901	E073	-45944
chr11	11430927	11431272	E073	-45573
chr11	11431306	11431861	E073	-44984
chr11	11447430	11447766	E073	-29079
chr11	11447838	11448430	E073	-28415
chr11	11448627	11449448	E073	-27397
chr11	11449456	11449765	E073	-27080
chr11	11450172	11450222	E073	-26623
chr11	11455411	11455546	E073	-21299
chr11	11455630	11455818	E073	-21027
chr11	11455942	11455992	E073	-20853
chr11	11456075	11456128	E073	-20717
chr11	11456593	11456643	E073	-20202
chr11	11457154	11457469	E073	-19376
chr11	11457484	11457611	E073	-19234
chr11	11457649	11457763	E073	-19082
chr11	11457901	11457996	E073	-18849
chr11	11458094	11458155	E073	-18690
chr11	11458172	11458319	E073	-18526
chr11	11458345	11458480	E073	-18365
chr11	11458483	11458764	E073	-18081
chr11	11464261	11464327	E073	-12518
chr11	11464340	11464641	E073	-12204
chr11	11464692	11464795	E073	-12050
chr11	11465814	11466693	E073	-10152
chr11	11467046	11467398	E073	-9447
chr11	11467436	11467584	E073	-9261
chr11	11478345	11478403	E073	1500
chr11	11478456	11478537	E073	1611
chr11	11478596	11478680	E073	1751
chr11	11481980	11482290	E073	5135
chr11	11482494	11483657	E073	5649
chr11	11484527	11484659	E073	7682
chr11	11484683	11486101	E073	7838
chr11	11490604	11490849	E073	13759
chr11	11491106	11491217	E073	14261
chr11	11500278	11500491	E073	23433
chr11	11500521	11500658	E073	23676
chr11	11504759	11504964	E073	27914
chr11	11505106	11505214	E073	28261
chr11	11505270	11505369	E073	28425
chr11	11505408	11505472	E073	28563
chr11	11505567	11505607	E073	28722
chr11	11512819	11512904	E073	35974
chr11	11512905	11513005	E073	36060
chr11	11513186	11513329	E073	36341
chr11	11522134	11522219	E073	45289
chr11	11522364	11522602	E073	45519
chr11	11523093	11523327	E073	46248
chr11	11523334	11524675	E073	46489
chr11	11428345	11428461	E074	-48384
chr11	11428499	11429530	E074	-47315
chr11	11431306	11431861	E074	-44984
chr11	11437527	11437974	E074	-38871
chr11	11438117	11438842	E074	-38003
chr11	11449456	11449765	E074	-27080
chr11	11457484	11457611	E074	-19234
chr11	11457649	11457763	E074	-19082
chr11	11457901	11457996	E074	-18849
chr11	11458094	11458155	E074	-18690
chr11	11458172	11458319	E074	-18526
chr11	11458345	11458480	E074	-18365
chr11	11458483	11458764	E074	-18081
chr11	11465814	11466693	E074	-10152
chr11	11481980	11482290	E074	5135
chr11	11523093	11523327	E074	46248
chr11	11523334	11524675	E074	46489
chr11	11428345	11428461	E081	-48384
chr11	11444714	11444854	E081	-31991
chr11	11444858	11444958	E081	-31887
chr11	11444989	11445053	E081	-31792
chr11	11464261	11464327	E081	-12518
chr11	11464340	11464641	E081	-12204
chr11	11464692	11464795	E081	-12050
chr11	11481980	11482290	E081	5135
chr11	11482494	11483657	E081	5649
chr11	11491106	11491217	E081	14261
chr11	11519031	11519081	E081	42186
chr11	11519212	11519743	E081	42367
chr11	11519833	11519957	E081	42988
chr11	11520044	11520094	E081	43199
chr11	11520382	11520561	E081	43537
chr11	11520793	11520872	E081	43948
chr11	11520940	11521060	E081	44095
chr11	11521106	11521268	E081	44261
chr11	11521311	11521406	E081	44466
chr11	11523093	11523327	E081	46248
chr11	11523334	11524675	E081	46489
chr11	11441865	11441975	E082	-34870
chr11	11443758	11443829	E082	-33016
chr11	11443896	11444662	E082	-32183
chr11	11481980	11482290	E082	5135
chr11	11482494	11483657	E082	5649