rs2797533

Organism: Homo sapiens

Alleles: C>G / C>T

Gene : Feature

LOC107985174 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0324 (9703/29912,GnomAD)
C==0358 (10444/29118,TOPMED)
C==0367 (1839/5008,1000G)
C==0327 (1262/3854,ALSPAC)
C==0327 (1211/3708,TWINSUK)

Position: chr1:110644162 (GRCh38.p7) (1p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 331 Enhancers around

Promoter: 32 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.110644162C>G
GRCh38.p7 chr 1	NC_000001.11:g.110644162C>T
GRCh37.p13 chr 1	NC_000001.10:g.111186784C>G
GRCh37.p13 chr 1	NC_000001.10:g.111186784C>T

Gene: LOC107985174, uncharacterized LOC107985174(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985174 transcript variant X1	XR_001738182.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X2	XR_001738183.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X3	XR_001738184.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X4	XR_001738185.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X5	XR_001738186.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X6	XR_001738187.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.343	T=0.657
1000Genomes	American	Sub	694	C=0.300	T=0.700
1000Genomes	East Asian	Sub	1008	C=0.420	T=0.580
1000Genomes	Europe	Sub	1006	C=0.285	T=0.715
1000Genomes	Global	Study-wide	5008	C=0.367	T=0.633
1000Genomes	South Asian	Sub	978	C=0.480	T=0.520
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.327	T=0.673
The Genome Aggregation Database	African	Sub	8692	C=0.351	T=0.649
The Genome Aggregation Database	American	Sub	836	C=0.260	T=0.74,
The Genome Aggregation Database	East Asian	Sub	1616	C=0.434	T=0.566
The Genome Aggregation Database	Europe	Sub	18466	C=0.305	T=0.695
The Genome Aggregation Database	Global	Study-wide	29912	C=0.324	T=0.675
The Genome Aggregation Database	Other	Sub	302	C=0.330	T=0.67,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.358	T=0.641
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.327	T=0.673

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
rs2797533	0.00046	alcohol dependence	20201924

eQTL of rs2797533 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:111186784	RP11-284N8.3	ENSG00000259834.1	C>T	2.1757e-2	-12878	Cerebellum

meQTL of rs2797533 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 )
chr1	43756213	43756316	E067	-42032
chr1	43756832	43756927	E067	-41421
chr1	43757920	43758173	E067	-40175
chr1	43758211	43758264	E067	-40084
chr1	43758778	43758856	E067	-39492
chr1	43758917	43759244	E067	-39104
chr1	43759670	43759949	E067	-38399
chr1	43760144	43760421	E067	-37927
chr1	43760549	43760644	E067	-37704
chr1	43761135	43761693	E067	-36655
chr1	43761819	43761869	E067	-36479
chr1	43761969	43762130	E067	-36218
chr1	43762591	43762631	E067	-35717
chr1	43762708	43762797	E067	-35551
chr1	43762962	43763357	E067	-34991
chr1	43764885	43765052	E067	-33296
chr1	43765073	43765133	E067	-33215
chr1	43765168	43765356	E067	-32992
chr1	43768524	43769022	E067	-29326
chr1	43769079	43769334	E067	-29014
chr1	43769583	43769743	E067	-28605
chr1	43770002	43770101	E067	-28247
chr1	43770146	43770358	E067	-27990
chr1	43780857	43780919	E067	-17429
chr1	43781298	43781468	E067	-16880
chr1	43782486	43782580	E067	-15768
chr1	43782691	43782762	E067	-15586
chr1	43783932	43784149	E067	-14199
chr1	43789969	43790053	E067	-8295
chr1	43790194	43790450	E067	-7898
chr1	43790583	43790709	E067	-7639
chr1	43809919	43810364	E067	11571
chr1	43810791	43811232	E067	12443
chr1	43811974	43812024	E067	13626
chr1	43813795	43813948	E067	15447
chr1	43831097	43831162	E067	32749
chr1	43831180	43831240	E067	32832
chr1	43831246	43831300	E067	32898
chr1	43831428	43831509	E067	33080
chr1	43831730	43831881	E067	33382
chr1	43836286	43836336	E067	37938
chr1	43836393	43836627	E067	38045
chr1	43836664	43836744	E067	38316
chr1	43838110	43838518	E067	39762
chr1	43838526	43839231	E067	40178
chr1	43839302	43839471	E067	40954
chr1	43842523	43842641	E067	44175
chr1	43846147	43846217	E067	47799
chr1	43847206	43847619	E067	48858
chr1	43753808	43753969	E068	-44379
chr1	43754222	43754378	E068	-43970
chr1	43754605	43754660	E068	-43688
chr1	43754770	43754868	E068	-43480
chr1	43755077	43755279	E068	-43069
chr1	43756832	43756927	E068	-41421
chr1	43757920	43758173	E068	-40175
chr1	43758211	43758264	E068	-40084
chr1	43758778	43758856	E068	-39492
chr1	43758917	43759244	E068	-39104
chr1	43759670	43759949	E068	-38399
chr1	43760144	43760421	E068	-37927
chr1	43760549	43760644	E068	-37704
chr1	43761135	43761693	E068	-36655
chr1	43761819	43761869	E068	-36479
chr1	43761969	43762130	E068	-36218
chr1	43762591	43762631	E068	-35717
chr1	43762708	43762797	E068	-35551
chr1	43762962	43763357	E068	-34991
chr1	43764885	43765052	E068	-33296
chr1	43765073	43765133	E068	-33215
chr1	43765168	43765356	E068	-32992
chr1	43768524	43769022	E068	-29326
chr1	43769079	43769334	E068	-29014
chr1	43769583	43769743	E068	-28605
chr1	43770002	43770101	E068	-28247
chr1	43770146	43770358	E068	-27990
chr1	43780098	43780183	E068	-18165
chr1	43780857	43780919	E068	-17429
chr1	43781298	43781468	E068	-16880
chr1	43782486	43782580	E068	-15768
chr1	43782691	43782762	E068	-15586
chr1	43783932	43784149	E068	-14199
chr1	43809919	43810364	E068	11571
chr1	43813635	43813703	E068	15287
chr1	43813795	43813948	E068	15447
chr1	43831180	43831240	E068	32832
chr1	43831246	43831300	E068	32898
chr1	43831428	43831509	E068	33080
chr1	43831730	43831881	E068	33382
chr1	43836286	43836336	E068	37938
chr1	43836393	43836627	E068	38045
chr1	43836664	43836744	E068	38316
chr1	43839302	43839471	E068	40954
chr1	43842523	43842641	E068	44175
chr1	43843609	43843813	E068	45261
chr1	43844305	43844355	E068	45957
chr1	43846147	43846217	E068	47799
chr1	43753808	43753969	E069	-44379
chr1	43754222	43754378	E069	-43970
chr1	43754605	43754660	E069	-43688
chr1	43754770	43754868	E069	-43480
chr1	43755077	43755279	E069	-43069
chr1	43756213	43756316	E069	-42032
chr1	43756832	43756927	E069	-41421
chr1	43757920	43758173	E069	-40175
chr1	43758211	43758264	E069	-40084
chr1	43758778	43758856	E069	-39492
chr1	43758917	43759244	E069	-39104
chr1	43759670	43759949	E069	-38399
chr1	43760144	43760421	E069	-37927
chr1	43760549	43760644	E069	-37704
chr1	43761819	43761869	E069	-36479
chr1	43761969	43762130	E069	-36218
chr1	43762591	43762631	E069	-35717
chr1	43762708	43762797	E069	-35551
chr1	43762962	43763357	E069	-34991
chr1	43765168	43765356	E069	-32992
chr1	43768524	43769022	E069	-29326
chr1	43769079	43769334	E069	-29014
chr1	43769583	43769743	E069	-28605
chr1	43770002	43770101	E069	-28247
chr1	43770146	43770358	E069	-27990
chr1	43780857	43780919	E069	-17429
chr1	43781298	43781468	E069	-16880
chr1	43782486	43782580	E069	-15768
chr1	43782691	43782762	E069	-15586
chr1	43783932	43784149	E069	-14199
chr1	43784959	43785013	E069	-13335
chr1	43787028	43787450	E069	-10898
chr1	43789814	43789874	E069	-8474
chr1	43789969	43790053	E069	-8295
chr1	43790194	43790450	E069	-7898
chr1	43809919	43810364	E069	11571
chr1	43813635	43813703	E069	15287
chr1	43831097	43831162	E069	32749
chr1	43831180	43831240	E069	32832
chr1	43831246	43831300	E069	32898
chr1	43836286	43836336	E069	37938
chr1	43836393	43836627	E069	38045
chr1	43836664	43836744	E069	38316
chr1	43837130	43837170	E069	38782
chr1	43838110	43838518	E069	39762
chr1	43838526	43839231	E069	40178
chr1	43839302	43839471	E069	40954
chr1	43842523	43842641	E069	44175
chr1	43844305	43844355	E069	45957
chr1	43846147	43846217	E069	47799
chr1	43847206	43847619	E069	48858
chr1	43831428	43831509	E070	33080
chr1	43753808	43753969	E071	-44379
chr1	43754222	43754378	E071	-43970
chr1	43754605	43754660	E071	-43688
chr1	43754770	43754868	E071	-43480
chr1	43755077	43755279	E071	-43069
chr1	43756832	43756927	E071	-41421
chr1	43757920	43758173	E071	-40175
chr1	43758211	43758264	E071	-40084
chr1	43758778	43758856	E071	-39492
chr1	43758917	43759244	E071	-39104
chr1	43759670	43759949	E071	-38399
chr1	43760144	43760421	E071	-37927
chr1	43760549	43760644	E071	-37704
chr1	43761135	43761693	E071	-36655
chr1	43761819	43761869	E071	-36479
chr1	43761969	43762130	E071	-36218
chr1	43762591	43762631	E071	-35717
chr1	43762708	43762797	E071	-35551
chr1	43762962	43763357	E071	-34991
chr1	43764020	43764075	E071	-34273
chr1	43764885	43765052	E071	-33296
chr1	43765073	43765133	E071	-33215
chr1	43765168	43765356	E071	-32992
chr1	43766114	43766679	E071	-31669
chr1	43768524	43769022	E071	-29326
chr1	43769079	43769334	E071	-29014
chr1	43769583	43769743	E071	-28605
chr1	43770146	43770358	E071	-27990
chr1	43780857	43780919	E071	-17429
chr1	43781298	43781468	E071	-16880
chr1	43782486	43782580	E071	-15768
chr1	43782691	43782762	E071	-15586
chr1	43783932	43784149	E071	-14199
chr1	43784959	43785013	E071	-13335
chr1	43789969	43790053	E071	-8295
chr1	43790194	43790450	E071	-7898
chr1	43790583	43790709	E071	-7639
chr1	43795820	43796389	E071	-1959
chr1	43809919	43810364	E071	11571
chr1	43813795	43813948	E071	15447
chr1	43825979	43826040	E071	27631
chr1	43831097	43831162	E071	32749
chr1	43836286	43836336	E071	37938
chr1	43836393	43836627	E071	38045
chr1	43836664	43836744	E071	38316
chr1	43837130	43837170	E071	38782
chr1	43838110	43838518	E071	39762
chr1	43838526	43839231	E071	40178
chr1	43839302	43839471	E071	40954
chr1	43842523	43842641	E071	44175
chr1	43844305	43844355	E071	45957
chr1	43846147	43846217	E071	47799
chr1	43753808	43753969	E072	-44379
chr1	43754222	43754378	E072	-43970
chr1	43754605	43754660	E072	-43688
chr1	43754770	43754868	E072	-43480
chr1	43756213	43756316	E072	-42032
chr1	43756832	43756927	E072	-41421
chr1	43757920	43758173	E072	-40175
chr1	43758211	43758264	E072	-40084
chr1	43758778	43758856	E072	-39492
chr1	43758917	43759244	E072	-39104
chr1	43759670	43759949	E072	-38399
chr1	43760144	43760421	E072	-37927
chr1	43760549	43760644	E072	-37704
chr1	43761135	43761693	E072	-36655
chr1	43761819	43761869	E072	-36479
chr1	43761969	43762130	E072	-36218
chr1	43762591	43762631	E072	-35717
chr1	43762708	43762797	E072	-35551
chr1	43762962	43763357	E072	-34991
chr1	43764885	43765052	E072	-33296
chr1	43765073	43765133	E072	-33215
chr1	43765168	43765356	E072	-32992
chr1	43766114	43766679	E072	-31669
chr1	43769583	43769743	E072	-28605
chr1	43770002	43770101	E072	-28247
chr1	43770146	43770358	E072	-27990
chr1	43779266	43779316	E072	-19032
chr1	43779544	43779730	E072	-18618
chr1	43780857	43780919	E072	-17429
chr1	43781298	43781468	E072	-16880
chr1	43782486	43782580	E072	-15768
chr1	43782691	43782762	E072	-15586
chr1	43783932	43784149	E072	-14199
chr1	43784959	43785013	E072	-13335
chr1	43789969	43790053	E072	-8295
chr1	43790194	43790450	E072	-7898
chr1	43790583	43790709	E072	-7639
chr1	43809919	43810364	E072	11571
chr1	43831180	43831240	E072	32832
chr1	43831246	43831300	E072	32898
chr1	43831428	43831509	E072	33080
chr1	43831730	43831881	E072	33382
chr1	43836286	43836336	E072	37938
chr1	43836393	43836627	E072	38045
chr1	43836664	43836744	E072	38316
chr1	43839302	43839471	E072	40954
chr1	43842523	43842641	E072	44175
chr1	43843609	43843813	E072	45261
chr1	43844305	43844355	E072	45957
chr1	43846147	43846217	E072	47799
chr1	43757920	43758173	E073	-40175
chr1	43758211	43758264	E073	-40084
chr1	43758778	43758856	E073	-39492
chr1	43758917	43759244	E073	-39104
chr1	43759670	43759949	E073	-38399
chr1	43760144	43760421	E073	-37927
chr1	43760549	43760644	E073	-37704
chr1	43761135	43761693	E073	-36655
chr1	43761819	43761869	E073	-36479
chr1	43761969	43762130	E073	-36218
chr1	43762591	43762631	E073	-35717
chr1	43762708	43762797	E073	-35551
chr1	43762962	43763357	E073	-34991
chr1	43768524	43769022	E073	-29326
chr1	43769079	43769334	E073	-29014
chr1	43769583	43769743	E073	-28605
chr1	43770002	43770101	E073	-28247
chr1	43770146	43770358	E073	-27990
chr1	43783932	43784149	E073	-14199
chr1	43784959	43785013	E073	-13335
chr1	43831097	43831162	E073	32749
chr1	43831180	43831240	E073	32832
chr1	43831246	43831300	E073	32898
chr1	43831428	43831509	E073	33080
chr1	43831730	43831881	E073	33382
chr1	43836286	43836336	E073	37938
chr1	43836393	43836627	E073	38045
chr1	43847206	43847619	E073	48858
chr1	43753808	43753969	E074	-44379
chr1	43754222	43754378	E074	-43970
chr1	43754605	43754660	E074	-43688
chr1	43754770	43754868	E074	-43480
chr1	43756213	43756316	E074	-42032
chr1	43756832	43756927	E074	-41421
chr1	43757920	43758173	E074	-40175
chr1	43758211	43758264	E074	-40084
chr1	43758778	43758856	E074	-39492
chr1	43758917	43759244	E074	-39104
chr1	43759670	43759949	E074	-38399
chr1	43760144	43760421	E074	-37927
chr1	43761135	43761693	E074	-36655
chr1	43761819	43761869	E074	-36479
chr1	43761969	43762130	E074	-36218
chr1	43762591	43762631	E074	-35717
chr1	43762708	43762797	E074	-35551
chr1	43762962	43763357	E074	-34991
chr1	43764020	43764075	E074	-34273
chr1	43764885	43765052	E074	-33296
chr1	43765073	43765133	E074	-33215
chr1	43765168	43765356	E074	-32992
chr1	43766114	43766679	E074	-31669
chr1	43769079	43769334	E074	-29014
chr1	43769583	43769743	E074	-28605
chr1	43780857	43780919	E074	-17429
chr1	43781298	43781468	E074	-16880
chr1	43782486	43782580	E074	-15768
chr1	43782691	43782762	E074	-15586
chr1	43783932	43784149	E074	-14199
chr1	43789814	43789874	E074	-8474
chr1	43789969	43790053	E074	-8295
chr1	43790194	43790450	E074	-7898
chr1	43790583	43790709	E074	-7639
chr1	43829898	43829975	E074	31550
chr1	43831097	43831162	E074	32749
chr1	43836286	43836336	E074	37938
chr1	43836393	43836627	E074	38045
chr1	43836664	43836744	E074	38316
chr1	43837130	43837170	E074	38782
chr1	43838110	43838518	E074	39762
chr1	43838526	43839231	E074	40178
chr1	43839302	43839471	E074	40954
chr1	43842523	43842641	E074	44175
chr1	43843609	43843813	E074	45261
chr1	43846147	43846217	E074	47799
chr1	43753808	43753969	E081	-44379
chr1	43754222	43754378	E081	-43970
chr1	43756213	43756316	E081	-42032
chr1	43783932	43784149	E081	-14199
chr1	43783932	43784149	E082	-14199
chr1	43813795	43813948	E082	15447

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	43814011	43816096	E067	15663
chr1	43823595	43825189	E067	25247
chr1	43831901	43834772	E067	33553
chr1	43767612	43767862	E068	-30486
chr1	43814011	43816096	E068	15663
chr1	43823595	43825189	E068	25247
chr1	43831901	43834772	E068	33553
chr1	43767612	43767862	E069	-30486
chr1	43814011	43816096	E069	15663
chr1	43823595	43825189	E069	25247
chr1	43831901	43834772	E069	33553
chr1	43814011	43816096	E070	15663
chr1	43823595	43825189	E070	25247
chr1	43831901	43834772	E070	33553
chr1	43767612	43767862	E071	-30486
chr1	43814011	43816096	E071	15663
chr1	43823595	43825189	E071	25247
chr1	43831901	43834772	E071	33553
chr1	43767612	43767862	E072	-30486
chr1	43814011	43816096	E072	15663
chr1	43823595	43825189	E072	25247
chr1	43831901	43834772	E072	33553
chr1	43814011	43816096	E073	15663
chr1	43823595	43825189	E073	25247
chr1	43831901	43834772	E073	33553
chr1	43767612	43767862	E074	-30486
chr1	43814011	43816096	E074	15663
chr1	43823595	43825189	E074	25247
chr1	43831901	43834772	E074	33553
chr1	43814011	43816096	E082	15663
chr1	43823595	43825189	E082	25247
chr1	43831901	43834772	E082	33553