rs17118349

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LINC01135 : Intron Variant
LOC105378753 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0013 (398/29976,GnomAD)
T=0019 (566/29118,TOPMED)
T=0014 (69/5008,1000G)

Position: chr1:58885471 (GRCh38.p7) (1p32.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 229 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.58885471C>T
GRCh37.p13 chr 1	NC_000001.10:g.59351143C>T

Gene: LINC01135, long intergenic non-protein coding RNA 1135(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01135 transcript variant 1	NR_034014.1:n.	N/A	Intron Variant
LINC01135 transcript variant 2	NR_034015.1:n.	N/A	Intron Variant
LINC01135 transcript variant 3	NR_108106.1:n.	N/A	Intron Variant

Gene: LOC105378753, uncharacterized LOC105378753(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378753 transcript variant X6	XR_001738077.1:n.	N/A	Intron Variant
LOC105378753 transcript variant X7	XR_001738078.1:n.	N/A	Intron Variant
LOC105378753 transcript variant X1	XR_947408.2:n.	N/A	Intron Variant
LOC105378753 transcript variant X3	XR_947409.2:n.	N/A	Intron Variant
LOC105378753 transcript variant X7	XR_947410.2:n.	N/A	Intron Variant
LOC105378753 transcript variant X5	XR_947411.2:n.	N/A	Intron Variant
LOC105378753 transcript variant X2	XR_947412.2:n.	N/A	Intron Variant
LOC105378753 transcript variant X6	XR_947413.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.949	T=0.051
1000Genomes	American	Sub	694	C=1.000	T=0.000
1000Genomes	East Asian	Sub	1008	C=1.000	T=0.000
1000Genomes	Europe	Sub	1006	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.986	T=0.014
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
The Genome Aggregation Database	African	Sub	8724	C=0.955	T=0.045
The Genome Aggregation Database	American	Sub	838	C=1.000	T=0.000
The Genome Aggregation Database	East Asian	Sub	1622	C=1.000	T=0.000
The Genome Aggregation Database	Europe	Sub	18490	C=1.000	T=0.000
The Genome Aggregation Database	Global	Study-wide	29976	C=0.986	T=0.013
The Genome Aggregation Database	Other	Sub	302	C=1.000	T=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.980	T=0.019

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
rs17118349	0.000807	alcohol dependence	20201924

eQTL of rs17118349 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 rs17118349 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	59314436	59315293	E067	-35850
chr1	59315350	59315438	E067	-35705
chr1	59320863	59320956	E067	-30187
chr1	59328872	59328926	E067	-22217
chr1	59329121	59329181	E067	-21962
chr1	59339893	59339943	E067	-11200
chr1	59339947	59340143	E067	-11000
chr1	59340156	59341377	E067	-9766
chr1	59348002	59348066	E067	-3077
chr1	59348182	59348485	E067	-2658
chr1	59348683	59349929	E067	-1214
chr1	59350320	59350384	E067	-759
chr1	59350450	59351556	E067	0
chr1	59351627	59352053	E067	484
chr1	59352361	59352648	E067	1218
chr1	59360800	59361003	E067	9657
chr1	59361209	59361259	E067	10066
chr1	59361866	59361923	E067	10723
chr1	59361995	59362705	E067	10852
chr1	59362946	59363026	E067	11803
chr1	59370294	59370359	E067	19151
chr1	59370417	59370714	E067	19274
chr1	59370863	59370940	E067	19720
chr1	59371007	59371067	E067	19864
chr1	59371197	59371314	E067	20054
chr1	59371406	59371582	E067	20263
chr1	59314436	59315293	E068	-35850
chr1	59315350	59315438	E068	-35705
chr1	59320863	59320956	E068	-30187
chr1	59321018	59321507	E068	-29636
chr1	59323843	59324372	E068	-26771
chr1	59324400	59324534	E068	-26609
chr1	59327877	59328043	E068	-23100
chr1	59328872	59328926	E068	-22217
chr1	59329121	59329181	E068	-21962
chr1	59339893	59339943	E068	-11200
chr1	59339947	59340143	E068	-11000
chr1	59340156	59341377	E068	-9766
chr1	59347596	59347656	E068	-3487
chr1	59347777	59347879	E068	-3264
chr1	59348002	59348066	E068	-3077
chr1	59348182	59348485	E068	-2658
chr1	59348683	59349929	E068	-1214
chr1	59350320	59350384	E068	-759
chr1	59350450	59351556	E068	0
chr1	59351627	59352053	E068	484
chr1	59352361	59352648	E068	1218
chr1	59359052	59359184	E068	7909
chr1	59359220	59359655	E068	8077
chr1	59360800	59361003	E068	9657
chr1	59361209	59361259	E068	10066
chr1	59361316	59361479	E068	10173
chr1	59361573	59361679	E068	10430
chr1	59361866	59361923	E068	10723
chr1	59361995	59362705	E068	10852
chr1	59362946	59363026	E068	11803
chr1	59363553	59363630	E068	12410
chr1	59364420	59365342	E068	13277
chr1	59365377	59365455	E068	14234
chr1	59365552	59366348	E068	14409
chr1	59371406	59371582	E068	20263
chr1	59371636	59371847	E068	20493
chr1	59371929	59371979	E068	20786
chr1	59314436	59315293	E069	-35850
chr1	59315350	59315438	E069	-35705
chr1	59318465	59318673	E069	-32470
chr1	59318694	59318864	E069	-32279
chr1	59319027	59319519	E069	-31624
chr1	59319566	59319663	E069	-31480
chr1	59321018	59321507	E069	-29636
chr1	59321604	59321729	E069	-29414
chr1	59327877	59328043	E069	-23100
chr1	59339257	59339613	E069	-11530
chr1	59339893	59339943	E069	-11200
chr1	59339947	59340143	E069	-11000
chr1	59340156	59341377	E069	-9766
chr1	59346995	59347562	E069	-3581
chr1	59347596	59347656	E069	-3487
chr1	59347777	59347879	E069	-3264
chr1	59348002	59348066	E069	-3077
chr1	59348182	59348485	E069	-2658
chr1	59348683	59349929	E069	-1214
chr1	59350320	59350384	E069	-759
chr1	59350450	59351556	E069	0
chr1	59351627	59352053	E069	484
chr1	59352361	59352648	E069	1218
chr1	59352837	59353069	E069	1694
chr1	59361995	59362705	E069	10852
chr1	59362946	59363026	E069	11803
chr1	59370294	59370359	E069	19151
chr1	59370417	59370714	E069	19274
chr1	59370863	59370940	E069	19720
chr1	59371007	59371067	E069	19864
chr1	59371197	59371314	E069	20054
chr1	59371406	59371582	E069	20263
chr1	59371636	59371847	E069	20493
chr1	59327877	59328043	E070	-23100
chr1	59339947	59340143	E070	-11000
chr1	59340156	59341377	E070	-9766
chr1	59314436	59315293	E071	-35850
chr1	59315350	59315438	E071	-35705
chr1	59318465	59318673	E071	-32470
chr1	59318694	59318864	E071	-32279
chr1	59319027	59319519	E071	-31624
chr1	59319566	59319663	E071	-31480
chr1	59320152	59320211	E071	-30932
chr1	59320275	59320596	E071	-30547
chr1	59320863	59320956	E071	-30187
chr1	59321018	59321507	E071	-29636
chr1	59327877	59328043	E071	-23100
chr1	59339257	59339613	E071	-11530
chr1	59339893	59339943	E071	-11200
chr1	59339947	59340143	E071	-11000
chr1	59348002	59348066	E071	-3077
chr1	59348182	59348485	E071	-2658
chr1	59348683	59349929	E071	-1214
chr1	59350320	59350384	E071	-759
chr1	59350450	59351556	E071	0
chr1	59351627	59352053	E071	484
chr1	59352361	59352648	E071	1218
chr1	59359052	59359184	E071	7909
chr1	59359220	59359655	E071	8077
chr1	59360800	59361003	E071	9657
chr1	59361209	59361259	E071	10066
chr1	59361316	59361479	E071	10173
chr1	59361573	59361679	E071	10430
chr1	59361866	59361923	E071	10723
chr1	59361995	59362705	E071	10852
chr1	59362946	59363026	E071	11803
chr1	59363553	59363630	E071	12410
chr1	59364420	59365342	E071	13277
chr1	59365377	59365455	E071	14234
chr1	59365552	59366348	E071	14409
chr1	59368405	59368747	E071	17262
chr1	59371007	59371067	E071	19864
chr1	59371197	59371314	E071	20054
chr1	59371406	59371582	E071	20263
chr1	59371636	59371847	E071	20493
chr1	59371929	59371979	E071	20786
chr1	59314436	59315293	E072	-35850
chr1	59318465	59318673	E072	-32470
chr1	59318694	59318864	E072	-32279
chr1	59319027	59319519	E072	-31624
chr1	59319566	59319663	E072	-31480
chr1	59323843	59324372	E072	-26771
chr1	59324400	59324534	E072	-26609
chr1	59327291	59327467	E072	-23676
chr1	59327877	59328043	E072	-23100
chr1	59339016	59339101	E072	-12042
chr1	59339893	59339943	E072	-11200
chr1	59339947	59340143	E072	-11000
chr1	59348002	59348066	E072	-3077
chr1	59348182	59348485	E072	-2658
chr1	59348683	59349929	E072	-1214
chr1	59350450	59351556	E072	0
chr1	59359220	59359655	E072	8077
chr1	59361866	59361923	E072	10723
chr1	59361995	59362705	E072	10852
chr1	59362946	59363026	E072	11803
chr1	59363553	59363630	E072	12410
chr1	59364420	59365342	E072	13277
chr1	59370294	59370359	E072	19151
chr1	59371406	59371582	E072	20263
chr1	59371636	59371847	E072	20493
chr1	59314436	59315293	E073	-35850
chr1	59315350	59315438	E073	-35705
chr1	59320863	59320956	E073	-30187
chr1	59323843	59324372	E073	-26771
chr1	59324400	59324534	E073	-26609
chr1	59340156	59341377	E073	-9766
chr1	59348182	59348485	E073	-2658
chr1	59348683	59349929	E073	-1214
chr1	59350320	59350384	E073	-759
chr1	59350450	59351556	E073	0
chr1	59351627	59352053	E073	484
chr1	59352361	59352648	E073	1218
chr1	59359052	59359184	E073	7909
chr1	59359220	59359655	E073	8077
chr1	59360800	59361003	E073	9657
chr1	59361209	59361259	E073	10066
chr1	59361316	59361479	E073	10173
chr1	59361573	59361679	E073	10430
chr1	59361866	59361923	E073	10723
chr1	59361995	59362705	E073	10852
chr1	59365377	59365455	E073	14234
chr1	59365552	59366348	E073	14409
chr1	59370294	59370359	E073	19151
chr1	59370863	59370940	E073	19720
chr1	59371007	59371067	E073	19864
chr1	59371197	59371314	E073	20054
chr1	59371406	59371582	E073	20263
chr1	59371636	59371847	E073	20493
chr1	59384952	59385073	E073	33809
chr1	59314436	59315293	E074	-35850
chr1	59315350	59315438	E074	-35705
chr1	59318465	59318673	E074	-32470
chr1	59318694	59318864	E074	-32279
chr1	59319027	59319519	E074	-31624
chr1	59319566	59319663	E074	-31480
chr1	59327877	59328043	E074	-23100
chr1	59339893	59339943	E074	-11200
chr1	59339947	59340143	E074	-11000
chr1	59340156	59341377	E074	-9766
chr1	59348002	59348066	E074	-3077
chr1	59348182	59348485	E074	-2658
chr1	59348683	59349929	E074	-1214
chr1	59350320	59350384	E074	-759
chr1	59350450	59351556	E074	0
chr1	59359052	59359184	E074	7909
chr1	59359220	59359655	E074	8077
chr1	59360800	59361003	E074	9657
chr1	59361209	59361259	E074	10066
chr1	59361316	59361479	E074	10173
chr1	59361573	59361679	E074	10430
chr1	59361866	59361923	E074	10723
chr1	59361995	59362705	E074	10852
chr1	59362946	59363026	E074	11803
chr1	59365377	59365455	E074	14234
chr1	59365552	59366348	E074	14409
chr1	59366507	59366570	E074	15364
chr1	59370417	59370714	E074	19274
chr1	59370863	59370940	E074	19720
chr1	59371007	59371067	E074	19864
chr1	59371197	59371314	E074	20054
chr1	59371406	59371582	E074	20263
chr1	59371636	59371847	E074	20493
chr1	59340156	59341377	E081	-9766
chr1	59384952	59385073	E081	33809
chr1	59340156	59341377	E082	-9766

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	59368799	59370190	E067	17656
chr1	59368799	59370190	E068	17656
chr1	59368799	59370190	E069	17656
chr1	59368799	59370190	E070	17656
chr1	59368799	59370190	E071	17656
chr1	59368799	59370190	E072	17656
chr1	59368799	59370190	E073	17656
chr1	59368799	59370190	E074	17656
chr1	59368799	59370190	E082	17656