rs17235985

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

LOC107984123 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0224 (6661/29686,GnomAD)
T=0215 (6279/29118,TOPMED)
T=0220 (1101/5008,1000G)
T=0328 (1265/3854,ALSPAC)
T=0321 (1191/3708,TWINSUK)

Position: chr7:135309545 (GRCh38.p7) (7q33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 107 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.135309545G>T
GRCh37.p13 chr 7	NC_000007.13:g.134994297G>T
SLC23A4P pseudogene	NG_006548.1:g.4117C>A

Gene: LOC107984123, uncharacterized LOC107984123(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107984123 transcript	XR_001745376.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.915	T=0.085
1000Genomes	American	Sub	694	G=0.780	T=0.220
1000Genomes	East Asian	Sub	1008	G=0.888	T=0.112
1000Genomes	Europe	Sub	1006	G=0.673	T=0.327
1000Genomes	Global	Study-wide	5008	G=0.780	T=0.220
1000Genomes	South Asian	Sub	978	G=0.600	T=0.400
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.672	T=0.328
The Genome Aggregation Database	African	Sub	8664	G=0.896	T=0.104
The Genome Aggregation Database	American	Sub	838	G=0.810	T=0.190
The Genome Aggregation Database	East Asian	Sub	1614	G=0.888	T=0.112
The Genome Aggregation Database	Europe	Sub	18270	G=0.708	T=0.291
The Genome Aggregation Database	Global	Study-wide	29686	G=0.775	T=0.224
The Genome Aggregation Database	Other	Sub	300	G=0.670	T=0.330
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.784	T=0.215
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.679	T=0.321

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs17235985	0.00013	alcohol dependence(early age of onset)	20201924
rs17235985	0.00099	alcohol dependence	20201924

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 )
chr7	134944944	134945267	E067	-49030
chr7	134945406	134945502	E067	-48795
chr7	134945681	134946590	E067	-47707
chr7	134946746	134946879	E067	-47418
chr7	134959165	134959737	E067	-34560
chr7	134959770	134959852	E067	-34445
chr7	135027132	135027182	E067	32835
chr7	135027268	135027320	E067	32971
chr7	135027384	135028670	E067	33087
chr7	134945406	134945502	E068	-48795
chr7	134946746	134946879	E068	-47418
chr7	134947033	134947118	E068	-47179
chr7	134947148	134947198	E068	-47099
chr7	134966119	134966768	E068	-27529
chr7	134966799	134966864	E068	-27433
chr7	134966884	134967048	E068	-27249
chr7	135005561	135005612	E068	11264
chr7	135006302	135006664	E068	12005
chr7	135006759	135006862	E068	12462
chr7	135006957	135007001	E068	12660
chr7	135027132	135027182	E068	32835
chr7	135027268	135027320	E068	32971
chr7	135027384	135028670	E068	33087
chr7	134944753	134944825	E069	-49472
chr7	134944944	134945267	E069	-49030
chr7	134945406	134945502	E069	-48795
chr7	134945681	134946590	E069	-47707
chr7	134946746	134946879	E069	-47418
chr7	134959165	134959737	E069	-34560
chr7	134959770	134959852	E069	-34445
chr7	134966799	134966864	E069	-27433
chr7	135027268	135027320	E069	32971
chr7	135027384	135028670	E069	33087
chr7	134945681	134946590	E070	-47707
chr7	134988474	134988574	E070	-5723
chr7	135004925	135005525	E070	10628
chr7	135005561	135005612	E070	11264
chr7	135006302	135006664	E070	12005
chr7	135006759	135006862	E070	12462
chr7	135006957	135007001	E070	12660
chr7	135019653	135019911	E070	25356
chr7	135019986	135020921	E070	25689
chr7	135027132	135027182	E070	32835
chr7	135027268	135027320	E070	32971
chr7	135027384	135028670	E070	33087
chr7	134944507	134944690	E071	-49607
chr7	134944753	134944825	E071	-49472
chr7	134944944	134945267	E071	-49030
chr7	134945406	134945502	E071	-48795
chr7	134946746	134946879	E071	-47418
chr7	134947852	134948010	E071	-46287
chr7	134948023	134948073	E071	-46224
chr7	134959165	134959737	E071	-34560
chr7	134959770	134959852	E071	-34445
chr7	134966799	134966864	E071	-27433
chr7	135027132	135027182	E071	32835
chr7	135027268	135027320	E071	32971
chr7	135027384	135028670	E071	33087
chr7	134944753	134944825	E072	-49472
chr7	134944944	134945267	E072	-49030
chr7	134945406	134945502	E072	-48795
chr7	134945681	134946590	E072	-47707
chr7	134946746	134946879	E072	-47418
chr7	134947033	134947118	E072	-47179
chr7	134947148	134947198	E072	-47099
chr7	134947852	134948010	E072	-46287
chr7	134948023	134948073	E072	-46224
chr7	134966799	134966864	E072	-27433
chr7	135027268	135027320	E072	32971
chr7	135027384	135028670	E072	33087
chr7	134945406	134945502	E073	-48795
chr7	134945681	134946590	E073	-47707
chr7	134946746	134946879	E073	-47418
chr7	134959165	134959737	E073	-34560
chr7	134959770	134959852	E073	-34445
chr7	135004925	135005525	E073	10628
chr7	135027268	135027320	E073	32971
chr7	135027384	135028670	E073	33087
chr7	134944944	134945267	E074	-49030
chr7	134945406	134945502	E074	-48795
chr7	134946746	134946879	E074	-47418
chr7	134966119	134966768	E074	-27529
chr7	134966799	134966864	E074	-27433
chr7	135027132	135027182	E074	32835
chr7	135027268	135027320	E074	32971
chr7	135027384	135028670	E074	33087
chr7	134966884	134967048	E081	-27249
chr7	134967365	134968080	E081	-26217
chr7	135024998	135025241	E081	30701
chr7	135025326	135025447	E081	31029
chr7	135025643	135025693	E081	31346
chr7	135025780	135026333	E081	31483
chr7	135026427	135026507	E081	32130
chr7	135026904	135026987	E081	32607
chr7	135027132	135027182	E081	32835
chr7	135027268	135027320	E081	32971
chr7	135027384	135028670	E081	33087
chr7	135028749	135028814	E081	34452
chr7	135031219	135031270	E081	36922
chr7	135006302	135006664	E082	12005
chr7	135006759	135006862	E082	12462
chr7	135025326	135025447	E082	31029
chr7	135025643	135025693	E082	31346
chr7	135025780	135026333	E082	31483
chr7	135027268	135027320	E082	32971
chr7	135027384	135028670	E082	33087
chr7	135028749	135028814	E082	34452

rs17235985

Genomic Coordinates

Gene: LOC107984123, uncharacterized LOC107984123(minus strand)

Population Frequency

P-Value

eQTL of rs17235985 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs17235985 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)