rs12074893

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

RLF : Intron Variant
LOC105378671 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0419 (12531/29886,GnomAD)
T=0441 (12851/29118,TOPMED)
T=0423 (2117/5008,1000G)
T=0323 (1246/3854,ALSPAC)
T=0320 (1187/3708,TWINSUK)

Position: chr1:40162447 (GRCh38.p7) (1p34.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 84 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.40162447C>T
GRCh37.p13 chr 1	NC_000001.10:g.40628119C>T

Gene: RLF, rearranged L-myc fusion(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RLF transcript	NM_012421.3:c.	N/A	Intron Variant
RLF transcript variant X1	XM_017002016.1:c.	N/A	Intron Variant
RLF transcript variant X2	XM_017002017.1:c.	N/A	Intron Variant
RLF transcript variant X3	XM_017002018.1:c.	N/A	Intron Variant

Gene: LOC105378671, uncharacterized LOC105378671(minus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378671 transcript	XR_947232.1:n.	N/A	Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.306	T=0.694
1000Genomes	American	Sub	694	C=0.650	T=0.350
1000Genomes	East Asian	Sub	1008	C=0.712	T=0.288
1000Genomes	Europe	Sub	1006	C=0.689	T=0.311
1000Genomes	Global	Study-wide	5008	C=0.577	T=0.423
1000Genomes	South Asian	Sub	978	C=0.640	T=0.360
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.677	T=0.323
The Genome Aggregation Database	African	Sub	8700	C=0.352	T=0.648
The Genome Aggregation Database	American	Sub	838	C=0.620	T=0.380
The Genome Aggregation Database	East Asian	Sub	1618	C=0.748	T=0.252
The Genome Aggregation Database	Europe	Sub	18428	C=0.668	T=0.331
The Genome Aggregation Database	Global	Study-wide	29886	C=0.580	T=0.419
The Genome Aggregation Database	Other	Sub	302	C=0.820	T=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.558	T=0.441
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.680	T=0.320

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
rs12074893	0.000443	alcohol dependence	20201924

eQTL of rs12074893 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 rs12074893 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg00695362	chr1:40506212	CAP1	-0.00780057634520619	4.0143e-9

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 )
chr1	40633059	40633099	E067	4940
chr1	40633168	40633235	E067	5049
chr1	40648626	40648922	E067	20507
chr1	40649131	40649220	E067	21012
chr1	40653449	40653499	E067	25330
chr1	40653676	40653756	E067	25557
chr1	40609647	40610040	E068	-18079
chr1	40629353	40629434	E068	1234
chr1	40629548	40629648	E068	1429
chr1	40629910	40630013	E068	1791
chr1	40630034	40630425	E068	1915
chr1	40630597	40630693	E068	2478
chr1	40630845	40630952	E068	2726
chr1	40631024	40631064	E068	2905
chr1	40631205	40631245	E068	3086
chr1	40633059	40633099	E068	4940
chr1	40633168	40633235	E068	5049
chr1	40649131	40649220	E068	21012
chr1	40649224	40649334	E068	21105
chr1	40653175	40653335	E068	25056
chr1	40653449	40653499	E068	25330
chr1	40653676	40653756	E068	25557
chr1	40629353	40629434	E069	1234
chr1	40633059	40633099	E069	4940
chr1	40633168	40633235	E069	5049
chr1	40648626	40648922	E069	20507
chr1	40649131	40649220	E069	21012
chr1	40649224	40649334	E069	21105
chr1	40653449	40653499	E069	25330
chr1	40653676	40653756	E069	25557
chr1	40598082	40598136	E070	-29983
chr1	40609395	40609628	E070	-18491
chr1	40609647	40610040	E070	-18079
chr1	40629353	40629434	E070	1234
chr1	40629548	40629648	E070	1429
chr1	40649131	40649220	E070	21012
chr1	40609395	40609628	E071	-18491
chr1	40629548	40629648	E071	1429
chr1	40629910	40630013	E071	1791
chr1	40630034	40630425	E071	1915
chr1	40630597	40630693	E071	2478
chr1	40630845	40630952	E071	2726
chr1	40631024	40631064	E071	2905
chr1	40648626	40648922	E071	20507
chr1	40649131	40649220	E071	21012
chr1	40649224	40649334	E071	21105
chr1	40651808	40651874	E071	23689
chr1	40652192	40652569	E071	24073
chr1	40653175	40653335	E071	25056
chr1	40653449	40653499	E071	25330
chr1	40653676	40653756	E071	25557
chr1	40676324	40676374	E071	48205
chr1	40609647	40610040	E072	-18079
chr1	40648626	40648922	E072	20507
chr1	40649131	40649220	E072	21012
chr1	40649224	40649334	E072	21105
chr1	40651808	40651874	E072	23689
chr1	40652192	40652569	E072	24073
chr1	40653449	40653499	E072	25330
chr1	40653676	40653756	E072	25557
chr1	40609647	40610040	E073	-18079
chr1	40648626	40648922	E073	20507
chr1	40649131	40649220	E073	21012
chr1	40649224	40649334	E073	21105
chr1	40651694	40651748	E073	23575
chr1	40651808	40651874	E073	23689
chr1	40652192	40652569	E073	24073
chr1	40629353	40629434	E074	1234
chr1	40629548	40629648	E074	1429
chr1	40629910	40630013	E074	1791
chr1	40630845	40630952	E074	2726
chr1	40648626	40648922	E074	20507
chr1	40649131	40649220	E074	21012
chr1	40653175	40653335	E074	25056
chr1	40653449	40653499	E074	25330
chr1	40653676	40653756	E074	25557
chr1	40629910	40630013	E081	1791
chr1	40651808	40651874	E081	23689
chr1	40652192	40652569	E081	24073
chr1	40629548	40629648	E082	1429
chr1	40629910	40630013	E082	1791
chr1	40633059	40633099	E082	4940
chr1	40633168	40633235	E082	5049
chr1	40652192	40652569	E082	24073

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	40598450	40598990	E067	-29129
chr1	40626494	40627900	E067	-219
chr1	40627915	40628047	E067	-72
chr1	40628053	40628244	E067	0
chr1	40628355	40628504	E067	236
chr1	40598450	40598990	E068	-29129
chr1	40626494	40627900	E068	-219
chr1	40627915	40628047	E068	-72
chr1	40628053	40628244	E068	0
chr1	40628355	40628504	E068	236
chr1	40598450	40598990	E069	-29129
chr1	40626494	40627900	E069	-219
chr1	40627915	40628047	E069	-72
chr1	40628053	40628244	E069	0
chr1	40628355	40628504	E069	236
chr1	40598450	40598990	E070	-29129
chr1	40626494	40627900	E070	-219
chr1	40627915	40628047	E070	-72
chr1	40628053	40628244	E070	0
chr1	40628355	40628504	E070	236
chr1	40598450	40598990	E071	-29129
chr1	40626494	40627900	E071	-219
chr1	40627915	40628047	E071	-72
chr1	40628053	40628244	E071	0
chr1	40628355	40628504	E071	236
chr1	40626494	40627900	E072	-219
chr1	40627915	40628047	E072	-72
chr1	40628053	40628244	E072	0
chr1	40628355	40628504	E072	236
chr1	40598450	40598990	E073	-29129
chr1	40626494	40627900	E073	-219
chr1	40627915	40628047	E073	-72
chr1	40628053	40628244	E073	0
chr1	40628355	40628504	E073	236
chr1	40598450	40598990	E074	-29129
chr1	40626494	40627900	E074	-219
chr1	40627915	40628047	E074	-72
chr1	40628053	40628244	E074	0
chr1	40628355	40628504	E074	236
chr1	40626494	40627900	E081	-219
chr1	40627915	40628047	E081	-72
chr1	40628053	40628244	E081	0
chr1	40628355	40628504	E081	236
chr1	40626494	40627900	E082	-219
chr1	40627915	40628047	E082	-72
chr1	40628053	40628244	E082	0
chr1	40628355	40628504	E082	236