rs4920422

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

LOC101927876 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0159 (4792/29960,GnomAD)
A=0167 (4864/29118,TOPMED)
A=0167 (836/5008,1000G)
A=0169 (652/3854,ALSPAC)
A=0156 (580/3708,TWINSUK)

Position: chr1:18066258 (GRCh38.p7) (1p36.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 81 Enhancers around

Promoter: 47 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.18066258C>A
GRCh37.p13 chr 1	NC_000001.10:g.18392752C>A

Gene: LOC101927876, uncharacterized LOC101927876(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01654 transcript	NR_125946.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.782	A=0.218
1000Genomes	American	Sub	694	C=0.870	A=0.130
1000Genomes	East Asian	Sub	1008	C=0.886	A=0.114
1000Genomes	Europe	Sub	1006	C=0.843	A=0.157
1000Genomes	Global	Study-wide	5008	C=0.833	A=0.167
1000Genomes	South Asian	Sub	978	C=0.810	A=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.831	A=0.169
The Genome Aggregation Database	African	Sub	8710	C=0.795	A=0.205
The Genome Aggregation Database	American	Sub	838	C=0.860	A=0.140
The Genome Aggregation Database	East Asian	Sub	1618	C=0.912	A=0.088
The Genome Aggregation Database	Europe	Sub	18492	C=0.853	A=0.146
The Genome Aggregation Database	Global	Study-wide	29960	C=0.840	A=0.159
The Genome Aggregation Database	Other	Sub	302	C=0.890	A=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.833	A=0.167
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.844	A=0.156

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs4920422	0.000252	alcohol dependence	21314694

eQTL of rs4920422 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 rs4920422 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	18385369	18385490	E067	-7262
chr1	18385582	18385731	E067	-7021
chr1	18385861	18385970	E067	-6782
chr1	18427000	18427455	E067	34248
chr1	18438337	18438472	E067	45585
chr1	18438572	18438622	E067	45820
chr1	18385582	18385731	E069	-7021
chr1	18438337	18438472	E069	45585
chr1	18438572	18438622	E069	45820
chr1	18358483	18358537	E070	-34215
chr1	18358669	18358725	E070	-34027
chr1	18384194	18384340	E070	-8412
chr1	18384802	18384936	E070	-7816
chr1	18385118	18385207	E070	-7545
chr1	18385369	18385490	E070	-7262
chr1	18386905	18387632	E070	-5120
chr1	18390724	18390774	E070	-1978
chr1	18391062	18391321	E070	-1431
chr1	18398553	18398611	E070	5801
chr1	18398633	18398805	E070	5881
chr1	18404954	18405028	E070	12202
chr1	18405225	18405335	E070	12473
chr1	18406450	18406528	E070	13698
chr1	18406647	18406754	E070	13895
chr1	18407118	18407293	E070	14366
chr1	18407387	18407433	E070	14635
chr1	18417152	18417620	E070	24400
chr1	18417854	18417917	E070	25102
chr1	18417925	18417975	E070	25173
chr1	18418142	18418271	E070	25390
chr1	18438337	18438472	E070	45585
chr1	18385582	18385731	E071	-7021
chr1	18438337	18438472	E071	45585
chr1	18438572	18438622	E071	45820
chr1	18433391	18433507	E072	40639
chr1	18438337	18438472	E072	45585
chr1	18438572	18438622	E072	45820
chr1	18385118	18385207	E073	-7545
chr1	18385369	18385490	E073	-7262
chr1	18385582	18385731	E073	-7021
chr1	18438337	18438472	E073	45585
chr1	18438572	18438622	E073	45820
chr1	18378954	18379517	E081	-13235
chr1	18379583	18379778	E081	-12974
chr1	18384802	18384936	E081	-7816
chr1	18385118	18385207	E081	-7545
chr1	18385369	18385490	E081	-7262
chr1	18385582	18385731	E081	-7021
chr1	18386905	18387632	E081	-5120
chr1	18398553	18398611	E081	5801
chr1	18398633	18398805	E081	5881
chr1	18399702	18399788	E081	6950
chr1	18400338	18400769	E081	7586
chr1	18400801	18400942	E081	8049
chr1	18405225	18405335	E081	12473
chr1	18406450	18406528	E081	13698
chr1	18406647	18406754	E081	13895
chr1	18407118	18407293	E081	14366
chr1	18407387	18407433	E081	14635
chr1	18417152	18417620	E081	24400
chr1	18417854	18417917	E081	25102
chr1	18417925	18417975	E081	25173
chr1	18418142	18418271	E081	25390
chr1	18418303	18418573	E081	25551
chr1	18425555	18425864	E081	32803
chr1	18426357	18426425	E081	33605
chr1	18433391	18433507	E081	40639
chr1	18433593	18433730	E081	40841
chr1	18438337	18438472	E081	45585
chr1	18438572	18438622	E081	45820
chr1	18386905	18387632	E082	-5120
chr1	18398051	18398101	E082	5299
chr1	18398553	18398611	E082	5801
chr1	18398633	18398805	E082	5881
chr1	18406450	18406528	E082	13698
chr1	18406647	18406754	E082	13895
chr1	18417152	18417620	E082	24400
chr1	18417854	18417917	E082	25102
chr1	18417925	18417975	E082	25173
chr1	18418142	18418271	E082	25390
chr1	18418303	18418573	E082	25551

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	18433793	18434371	E067	41041
chr1	18434620	18435196	E067	41868
chr1	18435251	18435388	E067	42499
chr1	18435458	18435574	E067	42706
chr1	18435659	18435823	E067	42907
chr1	18436479	18436531	E067	43727
chr1	18436546	18437025	E067	43794
chr1	18437039	18437348	E067	44287
chr1	18437562	18437862	E067	44810
chr1	18433793	18434371	E068	41041
chr1	18435251	18435388	E068	42499
chr1	18435458	18435574	E068	42706
chr1	18436479	18436531	E068	43727
chr1	18436546	18437025	E068	43794
chr1	18437039	18437348	E068	44287
chr1	18437562	18437862	E068	44810
chr1	18433793	18434371	E069	41041
chr1	18434620	18435196	E069	41868
chr1	18436546	18437025	E069	43794
chr1	18437039	18437348	E069	44287
chr1	18437562	18437862	E069	44810
chr1	18433793	18434371	E070	41041
chr1	18434620	18435196	E071	41868
chr1	18434620	18435196	E072	41868
chr1	18435251	18435388	E072	42499
chr1	18435458	18435574	E072	42706
chr1	18435659	18435823	E072	42907
chr1	18436479	18436531	E072	43727
chr1	18436546	18437025	E072	43794
chr1	18437039	18437348	E072	44287
chr1	18437562	18437862	E072	44810
chr1	18433793	18434371	E073	41041
chr1	18434620	18435196	E073	41868
chr1	18435251	18435388	E073	42499
chr1	18435458	18435574	E073	42706
chr1	18435659	18435823	E073	42907
chr1	18436479	18436531	E073	43727
chr1	18436546	18437025	E073	43794
chr1	18437039	18437348	E073	44287
chr1	18433793	18434371	E074	41041
chr1	18436479	18436531	E074	43727
chr1	18436546	18437025	E074	43794
chr1	18437039	18437348	E074	44287
chr1	18433793	18434371	E082	41041
chr1	18434620	18435196	E082	41868
chr1	18436479	18436531	E082	43727
chr1	18437562	18437862	E082	44810