rs6804367

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

FAM86JP : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0133 (3994/29936,GnomAD)
T=0178 (5182/29118,TOPMED)
T=0164 (819/5008,1000G)
T=0116 (447/3854,ALSPAC)
T=0104 (387/3708,TWINSUK)

Position: chr3:125921068 (GRCh38.p7) (3q21.2)

Phenotype: CD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 24 Enhancers around

Promoter: 45 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.125921068C>T
GRCh37.p13 chr 3	NC_000003.11:g.125639911C>T

Molecule type	Change	Amino acid[Codon]	SO Term
FAM86JP transcript variant 2	NR_024250.1:n.	N/A	Intron Variant
FAM86JP transcript variant 1	NR_024251.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.685	T=0.315
1000Genomes	American	Sub	694	C=0.880	T=0.120
1000Genomes	East Asian	Sub	1008	C=0.920	T=0.080
1000Genomes	Europe	Sub	1006	C=0.861	T=0.139
1000Genomes	Global	Study-wide	5008	C=0.836	T=0.164
1000Genomes	South Asian	Sub	978	C=0.900	T=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.884	T=0.116
The Genome Aggregation Database	African	Sub	8702	C=0.739	T=0.261
The Genome Aggregation Database	American	Sub	838	C=0.890	T=0.110
The Genome Aggregation Database	East Asian	Sub	1622	C=0.946	T=0.054
The Genome Aggregation Database	Europe	Sub	18472	C=0.919	T=0.080
The Genome Aggregation Database	Global	Study-wide	29936	C=0.866	T=0.133
The Genome Aggregation Database	Other	Sub	302	C=0.830	T=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.822	T=0.178
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.896	T=0.104

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

SNP ID	p-value	Traits	Study
rs6804367	0.000191	cocaine dependence	23958962

eQTL of rs6804367 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	1.3327e-16	4448	Cerebellum
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	3.9838e-21	4448	Frontal_Cortex_BA9
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	3.9379e-13	4448	Hypothalamus
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	2.0000e-27	4448	Cortex
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	4.9769e-18	4448	Cerebellar_Hemisphere
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	5.5250e-25	4448	Caudate_basal_ganglia
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	1.3705e-11	4448	Hippocampus
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	1.4218e-7	4448	Substantia_nigra
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	5.8053e-14	4448	Putamen_basal_ganglia
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	3.5190e-17	4448	Anterior_cingulate_cortex
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	2.2078e-23	4448	Nucleus_accumbens_basal_ganglia
Chr3:125639911	FAM86JP	ENSG00000171084.11	C>T	6.3847e-10	4448	Amygdala

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr3	125647728	125647881	E067	7817
chr3	125633318	125633439	E068	-6472
chr3	125633501	125633566	E068	-6345
chr3	125604757	125604851	E069	-35060
chr3	125647434	125647502	E069	7523
chr3	125647728	125647881	E069	7817
chr3	125604916	125605289	E070	-34622
chr3	125605357	125605592	E070	-34319
chr3	125647434	125647502	E070	7523
chr3	125647728	125647881	E070	7817
chr3	125604757	125604851	E071	-35060
chr3	125604916	125605289	E071	-34622
chr3	125605357	125605592	E071	-34319
chr3	125633318	125633439	E071	-6472
chr3	125633501	125633566	E071	-6345
chr3	125647434	125647502	E071	7523
chr3	125604757	125604851	E072	-35060
chr3	125604916	125605289	E072	-34622
chr3	125605357	125605592	E072	-34319
chr3	125633318	125633439	E072	-6472
chr3	125633501	125633566	E072	-6345
chr3	125604757	125604851	E081	-35060
chr3	125604916	125605289	E081	-34622
chr3	125605357	125605592	E081	-34319

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	125634009	125634308	E067	-5603
chr3	125634387	125634602	E067	-5309
chr3	125634666	125635863	E067	-4048
chr3	125635916	125636311	E067	-3600
chr3	125633639	125633698	E068	-6213
chr3	125633795	125633897	E068	-6014
chr3	125634009	125634308	E068	-5603
chr3	125634387	125634602	E068	-5309
chr3	125634666	125635863	E068	-4048
chr3	125635916	125636311	E068	-3600
chr3	125634009	125634308	E069	-5603
chr3	125634387	125634602	E069	-5309
chr3	125634666	125635863	E069	-4048
chr3	125635916	125636311	E069	-3600
chr3	125633795	125633897	E070	-6014
chr3	125634009	125634308	E070	-5603
chr3	125634387	125634602	E070	-5309
chr3	125634666	125635863	E070	-4048
chr3	125635916	125636311	E070	-3600
chr3	125633639	125633698	E071	-6213
chr3	125633795	125633897	E071	-6014
chr3	125634009	125634308	E071	-5603
chr3	125634387	125634602	E071	-5309
chr3	125634666	125635863	E071	-4048
chr3	125635916	125636311	E071	-3600
chr3	125633795	125633897	E072	-6014
chr3	125634009	125634308	E072	-5603
chr3	125634387	125634602	E072	-5309
chr3	125634666	125635863	E072	-4048
chr3	125635916	125636311	E072	-3600
chr3	125634009	125634308	E073	-5603
chr3	125634387	125634602	E073	-5309
chr3	125634666	125635863	E073	-4048
chr3	125635916	125636311	E073	-3600
chr3	125634009	125634308	E074	-5603
chr3	125634387	125634602	E074	-5309
chr3	125634666	125635863	E074	-4048
chr3	125635916	125636311	E074	-3600
chr3	125634009	125634308	E081	-5603
chr3	125633639	125633698	E082	-6213
chr3	125633795	125633897	E082	-6014
chr3	125634009	125634308	E082	-5603
chr3	125634387	125634602	E082	-5309
chr3	125634666	125635863	E082	-4048
chr3	125635916	125636311	E082	-3600