rs3850855

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

ZSWIM5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0350 (10477/29938,GnomAD)
T==0396 (11543/29118,TOPMED)
T==0290 (1451/5008,1000G)
T==0279 (1075/3854,ALSPAC)
T==0283 (1050/3708,TWINSUK)

Position: chr1:45058221 (GRCh38.p7) (1p34.1)

Phenotype: CD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 50 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.45058221T>C
GRCh37.p13 chr 1	NC_000001.10:g.45523893T>C

Gene: ZSWIM5, zinc finger SWIM-type containing 5(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZSWIM5 transcript	NM_020883.1:c.	N/A	Intron Variant
ZSWIM5 transcript variant X2	XM_011541861.2:c.	N/A	Intron Variant
ZSWIM5 transcript variant X1	XM_017001913.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.592	C=0.408
1000Genomes	American	Sub	694	T=0.220	C=0.780
1000Genomes	East Asian	Sub	1008	T=0.132	C=0.868
1000Genomes	Europe	Sub	1006	T=0.257	C=0.743
1000Genomes	Global	Study-wide	5008	T=0.290	C=0.710
1000Genomes	South Asian	Sub	978	T=0.130	C=0.870
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.279	C=0.721
The Genome Aggregation Database	African	Sub	8702	T=0.565	C=0.435
The Genome Aggregation Database	American	Sub	836	T=0.220	C=0.780
The Genome Aggregation Database	East Asian	Sub	1618	T=0.122	C=0.878
The Genome Aggregation Database	Europe	Sub	18480	T=0.276	C=0.723
The Genome Aggregation Database	Global	Study-wide	29938	T=0.350	C=0.650
The Genome Aggregation Database	Other	Sub	302	T=0.220	C=0.780
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.396	C=0.603
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.283	C=0.717

PMID	Title	Author	Journal
23958962	Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.	Gelernter J	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs3850855	0.00000609	cocaine dependence	23958962
rs3850855	0.000545	cocaine dependence	23958962

eQTL of rs3850855 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 rs3850855 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	45479046	45479114	E067	-44779
chr1	45479506	45479578	E067	-44315
chr1	45484156	45484206	E067	-39687
chr1	45484265	45484730	E067	-39163
chr1	45479506	45479578	E068	-44315
chr1	45479646	45479795	E068	-44098
chr1	45479860	45479958	E068	-43935
chr1	45480065	45480680	E068	-43213
chr1	45475404	45475458	E069	-48435
chr1	45480065	45480680	E069	-43213
chr1	45484156	45484206	E069	-39687
chr1	45484265	45484730	E069	-39163
chr1	45474672	45474739	E070	-49154
chr1	45479046	45479114	E070	-44779
chr1	45479243	45479373	E070	-44520
chr1	45479506	45479578	E070	-44315
chr1	45479646	45479795	E070	-44098
chr1	45479860	45479958	E070	-43935
chr1	45480065	45480680	E070	-43213
chr1	45484156	45484206	E070	-39687
chr1	45484265	45484730	E070	-39163
chr1	45485132	45485172	E070	-38721
chr1	45562861	45562919	E070	38968
chr1	45569300	45569508	E070	45407
chr1	45570199	45570287	E070	46306
chr1	45479046	45479114	E071	-44779
chr1	45480065	45480680	E071	-43213
chr1	45484156	45484206	E071	-39687
chr1	45484265	45484730	E071	-39163
chr1	45475404	45475458	E072	-48435
chr1	45479046	45479114	E072	-44779
chr1	45480065	45480680	E072	-43213
chr1	45480873	45480917	E072	-42976
chr1	45484156	45484206	E072	-39687
chr1	45484265	45484730	E072	-39163
chr1	45474672	45474739	E073	-49154
chr1	45475404	45475458	E073	-48435
chr1	45479243	45479373	E073	-44520
chr1	45479506	45479578	E073	-44315
chr1	45479646	45479795	E073	-44098
chr1	45479860	45479958	E073	-43935
chr1	45484265	45484730	E073	-39163
chr1	45475404	45475458	E074	-48435
chr1	45480065	45480680	E074	-43213
chr1	45484156	45484206	E074	-39687
chr1	45484265	45484730	E074	-39163
chr1	45475404	45475458	E081	-48435
chr1	45480065	45480680	E081	-43213
chr1	45479046	45479114	E082	-44779
chr1	45479243	45479373	E082	-44520

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	45476099	45478782	E067	-45111
chr1	45476099	45478782	E068	-45111
chr1	45476099	45478782	E069	-45111
chr1	45476099	45478782	E070	-45111
chr1	45476099	45478782	E071	-45111
chr1	45476099	45478782	E072	-45111
chr1	45476099	45478782	E073	-45111
chr1	45476099	45478782	E074	-45111
chr1	45476099	45478782	E081	-45111
chr1	45476099	45478782	E082	-45111