rs4849770

Organism: Homo sapiens

Alleles: G>A / G>C

Gene : Feature

LOC107985941 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0335 (10050/29916,GnomAD)
A=0359 (10471/29116,TOPMED)
A=0322 (1614/5008,1000G)
A=0330 (1271/3854,ALSPAC)
A=0345 (1278/3708,TWINSUK)

Position: chr2:119199450 (GRCh38.p7) (2q14.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 65 Enhancers around

Promoter: 45 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.119199450G>A
GRCh38.p7 chr 2	NC_000002.12:g.119199450G>C
GRCh37.p13 chr 2	NC_000002.11:g.119957026G>A
GRCh37.p13 chr 2	NC_000002.11:g.119957026G>C

Gene: LOC107985941, uncharacterized LOC107985941(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985941 transcript	XR_001739665.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.609	A=0.391
1000Genomes	American	Sub	694	G=0.630	A=0.370
1000Genomes	East Asian	Sub	1008	G=0.748	A=0.252
1000Genomes	Europe	Sub	1006	G=0.687	A=0.313
1000Genomes	Global	Study-wide	5008	G=0.678	A=0.322
1000Genomes	South Asian	Sub	978	G=0.720	A=0.280
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.670	A=0.330
The Genome Aggregation Database	African	Sub	8706	G=0.644	C=0.000
The Genome Aggregation Database	American	Sub	836	G=0.680	C=0.00,
The Genome Aggregation Database	East Asian	Sub	1618	G=0.703	C=0.000
The Genome Aggregation Database	Europe	Sub	18454	G=0.668	C=0.000
The Genome Aggregation Database	Global	Study-wide	29916	G=0.664	C=0.000
The Genome Aggregation Database	Other	Sub	302	G=0.710	C=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.640	A=0.359
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.655	A=0.345

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

SNP ID	p-value	Traits	Study
rs4849770	0.000188	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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 )
chr2	72418496	72418623	E067	3735
chr2	72418713	72418881	E067	3952
chr2	72430507	72430591	E067	15746
chr2	72431211	72431337	E067	16450
chr2	72431365	72431428	E067	16604
chr2	72431503	72433034	E067	16742
chr2	72433036	72433127	E067	18275
chr2	72463657	72463893	E067	48896
chr2	72463937	72464022	E067	49176
chr2	72400904	72401378	E068	-13383
chr2	72425857	72426337	E068	11096
chr2	72431211	72431337	E068	16450
chr2	72431365	72431428	E068	16604
chr2	72431503	72433034	E068	16742
chr2	72433036	72433127	E068	18275
chr2	72433252	72433302	E068	18491
chr2	72450002	72450601	E068	35241
chr2	72418496	72418623	E069	3735
chr2	72418713	72418881	E069	3952
chr2	72425857	72426337	E069	11096
chr2	72431365	72431428	E069	16604
chr2	72431503	72433034	E069	16742
chr2	72433036	72433127	E069	18275
chr2	72450002	72450601	E069	35241
chr2	72463657	72463893	E069	48896
chr2	72463937	72464022	E069	49176
chr2	72385445	72385528	E070	-29233
chr2	72412482	72412622	E071	-2139
chr2	72431365	72431428	E071	16604
chr2	72431503	72433034	E071	16742
chr2	72433036	72433127	E071	18275
chr2	72433252	72433302	E071	18491
chr2	72433590	72433695	E071	18829
chr2	72433742	72433837	E071	18981
chr2	72442932	72443225	E071	28171
chr2	72450002	72450601	E071	35241
chr2	72463265	72463344	E071	48504
chr2	72463657	72463893	E071	48896
chr2	72463937	72464022	E071	49176
chr2	72418343	72418464	E072	3582
chr2	72418496	72418623	E072	3735
chr2	72418713	72418881	E072	3952
chr2	72431365	72431428	E072	16604
chr2	72431503	72433034	E072	16742
chr2	72433036	72433127	E072	18275
chr2	72450002	72450601	E072	35241
chr2	72400904	72401378	E073	-13383
chr2	72431211	72431337	E073	16450
chr2	72431365	72431428	E073	16604
chr2	72431503	72433034	E073	16742
chr2	72433036	72433127	E073	18275
chr2	72365382	72365819	E074	-48942
chr2	72366093	72366160	E074	-48601
chr2	72400904	72401378	E074	-13383
chr2	72412482	72412622	E074	-2139
chr2	72418713	72418881	E074	3952
chr2	72430507	72430591	E074	15746
chr2	72431211	72431337	E074	16450
chr2	72431365	72431428	E074	16604
chr2	72431503	72433034	E074	16742
chr2	72433036	72433127	E074	18275
chr2	72433252	72433302	E074	18491
chr2	72441954	72442180	E074	27193
chr2	72450002	72450601	E074	35241
chr2	72368776	72368897	E082	-45864

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	72369878	72371358	E067	-43403
chr2	72371424	72373035	E067	-41726
chr2	72373036	72373229	E067	-41532
chr2	72373505	72375038	E067	-39723
chr2	72375104	72375264	E067	-39497
chr2	72375321	72375448	E067	-39313
chr2	72375531	72377989	E067	-36772
chr2	72369878	72371358	E068	-43403
chr2	72371424	72373035	E068	-41726
chr2	72373036	72373229	E068	-41532
chr2	72373505	72375038	E068	-39723
chr2	72375104	72375264	E068	-39497
chr2	72375321	72375448	E068	-39313
chr2	72375531	72377989	E068	-36772
chr2	72369878	72371358	E069	-43403
chr2	72371424	72373035	E069	-41726
chr2	72373036	72373229	E069	-41532
chr2	72375531	72377989	E069	-36772
chr2	72375104	72375264	E070	-39497
chr2	72375321	72375448	E070	-39313
chr2	72375531	72377989	E071	-36772
chr2	72369878	72371358	E072	-43403
chr2	72371424	72373035	E072	-41726
chr2	72375104	72375264	E072	-39497
chr2	72375321	72375448	E072	-39313
chr2	72375531	72377989	E072	-36772
chr2	72369878	72371358	E073	-43403
chr2	72371424	72373035	E073	-41726
chr2	72373505	72375038	E073	-39723
chr2	72375104	72375264	E073	-39497
chr2	72375321	72375448	E073	-39313
chr2	72375531	72377989	E073	-36772
chr2	72369878	72371358	E074	-43403
chr2	72371424	72373035	E074	-41726
chr2	72373036	72373229	E074	-41532
chr2	72373505	72375038	E074	-39723
chr2	72375104	72375264	E074	-39497
chr2	72375321	72375448	E074	-39313
chr2	72375531	72377989	E074	-36772
chr2	72371424	72373035	E082	-41726
chr2	72373036	72373229	E082	-41532
chr2	72373505	72375038	E082	-39723
chr2	72375104	72375264	E082	-39497
chr2	72375321	72375448	E082	-39313
chr2	72375531	72377989	E082	-36772

rs4849770

Genomic Coordinates

Gene: LOC107985941, uncharacterized LOC107985941(minus strand)

Population Frequency

P-Value

eQTL of rs4849770 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs4849770 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)