rs2149592

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

FSD1L : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0112 (3377/29972,GnomAD)
G=0147 (4300/29118,TOPMED)
G=0119 (595/5008,1000G)
G=0057 (221/3854,ALSPAC)
G=0058 (215/3708,TWINSUK)

Position: chr9:105467709 (GRCh38.p7) (9q31.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 140 Enhancers around

Promoter: 17 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.105467709A>G
GRCh37.p13 chr 9	NC_000009.11:g.108229990A>G

Gene: FSD1L, fibronectin type III and SPRY domain containing 1 like(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FSD1L transcript variant 3	NM_001145313.2:c.	N/A	Intron Variant
FSD1L transcript variant 4	NM_001287191.1:c.	N/A	Intron Variant
FSD1L transcript variant 5	NM_001287192.1:c.	N/A	Intron Variant
FSD1L transcript variant 2	NM_031919.4:c.	N/A	Intron Variant
FSD1L transcript variant X4	XM_005252254.2:c.	N/A	Intron Variant
FSD1L transcript variant X6	XM_005252257.3:c.	N/A	Intron Variant
FSD1L transcript variant X7	XM_005252260.3:c.	N/A	Intron Variant
FSD1L transcript variant X1	XM_011519077.2:c.	N/A	Intron Variant
FSD1L transcript variant X2	XM_011519078.2:c.	N/A	Intron Variant
FSD1L transcript variant X3	XM_011519079.2:c.	N/A	Intron Variant
FSD1L transcript variant X5	XM_017015182.1:c.	N/A	Intron Variant
FSD1L transcript variant X6	XM_017015183.1:c.	N/A	Intron Variant
FSD1L transcript variant X10	XM_017015185.1:c.	N/A	Intron Variant
FSD1L transcript variant X12	XM_017015187.1:c.	N/A	Intron Variant
FSD1L transcript variant X11	XM_011519080.2:c.	N/A	Genic Upstream Transcript Variant
FSD1L transcript variant X13	XM_011519081.2:c.	N/A	Genic Upstream Transcript Variant
FSD1L transcript variant X8	XM_017015184.1:c.	N/A	Genic Upstream Transcript Variant
FSD1L transcript variant X12	XM_017015186.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.715	G=0.285
1000Genomes	American	Sub	694	A=0.930	G=0.070
1000Genomes	East Asian	Sub	1008	A=1.000	G=0.000
1000Genomes	Europe	Sub	1006	A=0.925	G=0.075
1000Genomes	Global	Study-wide	5008	A=0.881	G=0.119
1000Genomes	South Asian	Sub	978	A=0.900	G=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.943	G=0.057
The Genome Aggregation Database	African	Sub	8716	A=0.746	G=0.254
The Genome Aggregation Database	American	Sub	836	A=0.950	G=0.050
The Genome Aggregation Database	East Asian	Sub	1622	A=1.000	G=0.000
The Genome Aggregation Database	Europe	Sub	18496	A=0.941	G=0.059
The Genome Aggregation Database	Global	Study-wide	29972	A=0.887	G=0.112
The Genome Aggregation Database	Other	Sub	302	A=0.910	G=0.090
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.852	G=0.147
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.942	G=0.058

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs2149592	1.17E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs2149592 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 rs2149592 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 )
chr9	108180672	108181782	E067	-48208
chr9	108181810	108181969	E067	-48021
chr9	108182176	108183027	E067	-46963
chr9	108193710	108195188	E067	-34802
chr9	108200220	108200273	E067	-29717
chr9	108200442	108201026	E067	-28964
chr9	108203995	108204145	E067	-25845
chr9	108204185	108204358	E067	-25632
chr9	108206499	108206788	E067	-23202
chr9	108206909	108207053	E067	-22937
chr9	108207338	108207535	E067	-22455
chr9	108207570	108208050	E067	-21940
chr9	108219553	108219639	E067	-10351
chr9	108219884	108220478	E067	-9512
chr9	108180672	108181782	E068	-48208
chr9	108181810	108181969	E068	-48021
chr9	108182176	108183027	E068	-46963
chr9	108203995	108204145	E068	-25845
chr9	108204185	108204358	E068	-25632
chr9	108207570	108208050	E068	-21940
chr9	108208304	108208390	E068	-21600
chr9	108219884	108220478	E068	-9512
chr9	108221590	108221722	E068	-8268
chr9	108221746	108222017	E068	-7973
chr9	108222053	108222390	E068	-7600
chr9	108242305	108242367	E068	12315
chr9	108180672	108181782	E069	-48208
chr9	108181810	108181969	E069	-48021
chr9	108182176	108183027	E069	-46963
chr9	108193710	108195188	E069	-34802
chr9	108200220	108200273	E069	-29717
chr9	108200442	108201026	E069	-28964
chr9	108201103	108201225	E069	-28765
chr9	108203598	108203806	E069	-26184
chr9	108203995	108204145	E069	-25845
chr9	108204185	108204358	E069	-25632
chr9	108205097	108205937	E069	-24053
chr9	108206909	108207053	E069	-22937
chr9	108207338	108207535	E069	-22455
chr9	108207570	108208050	E069	-21940
chr9	108208304	108208390	E069	-21600
chr9	108209288	108209338	E069	-20652
chr9	108209438	108209591	E069	-20399
chr9	108212340	108212436	E069	-17554
chr9	108213593	108213946	E069	-16044
chr9	108219553	108219639	E069	-10351
chr9	108219884	108220478	E069	-9512
chr9	108213593	108213946	E070	-16044
chr9	108180672	108181782	E071	-48208
chr9	108181810	108181969	E071	-48021
chr9	108182176	108183027	E071	-46963
chr9	108183569	108183728	E071	-46262
chr9	108183733	108183798	E071	-46192
chr9	108193710	108195188	E071	-34802
chr9	108200442	108201026	E071	-28964
chr9	108203598	108203806	E071	-26184
chr9	108203995	108204145	E071	-25845
chr9	108204185	108204358	E071	-25632
chr9	108207338	108207535	E071	-22455
chr9	108207570	108208050	E071	-21940
chr9	108208304	108208390	E071	-21600
chr9	108208421	108208539	E071	-21451
chr9	108219884	108220478	E071	-9512
chr9	108237610	108237901	E071	7620
chr9	108243028	108243170	E071	13038
chr9	108273749	108274124	E071	43759
chr9	108180672	108181782	E072	-48208
chr9	108181810	108181969	E072	-48021
chr9	108182176	108183027	E072	-46963
chr9	108193710	108195188	E072	-34802
chr9	108200220	108200273	E072	-29717
chr9	108203995	108204145	E072	-25845
chr9	108204185	108204358	E072	-25632
chr9	108205097	108205937	E072	-24053
chr9	108207338	108207535	E072	-22455
chr9	108207570	108208050	E072	-21940
chr9	108208304	108208390	E072	-21600
chr9	108212340	108212436	E072	-17554
chr9	108237610	108237901	E072	7620
chr9	108242788	108242838	E072	12798
chr9	108243028	108243170	E072	13038
chr9	108250606	108251024	E072	20616
chr9	108204185	108204358	E073	-25632
chr9	108207338	108207535	E073	-22455
chr9	108207570	108208050	E073	-21940
chr9	108208304	108208390	E073	-21600
chr9	108180672	108181782	E074	-48208
chr9	108181810	108181969	E074	-48021
chr9	108182176	108183027	E074	-46963
chr9	108193710	108195188	E074	-34802
chr9	108197312	108197431	E074	-32559
chr9	108197734	108197919	E074	-32071
chr9	108200442	108201026	E074	-28964
chr9	108201103	108201225	E074	-28765
chr9	108203598	108203806	E074	-26184
chr9	108203995	108204145	E074	-25845
chr9	108204185	108204358	E074	-25632
chr9	108205097	108205937	E074	-24053
chr9	108206499	108206788	E074	-23202
chr9	108206909	108207053	E074	-22937
chr9	108207338	108207535	E074	-22455
chr9	108207570	108208050	E074	-21940
chr9	108208304	108208390	E074	-21600
chr9	108219553	108219639	E074	-10351
chr9	108237610	108237901	E074	7620
chr9	108242788	108242838	E074	12798
chr9	108243028	108243170	E074	13038
chr9	108273749	108274124	E074	43759
chr9	108180672	108181782	E081	-48208
chr9	108181810	108181969	E081	-48021
chr9	108182176	108183027	E081	-46963
chr9	108192603	108192701	E081	-37289
chr9	108193710	108195188	E081	-34802
chr9	108195812	108195923	E081	-34067
chr9	108195972	108196012	E081	-33978
chr9	108203598	108203806	E081	-26184
chr9	108203995	108204145	E081	-25845
chr9	108204185	108204358	E081	-25632
chr9	108209288	108209338	E081	-20652
chr9	108209438	108209591	E081	-20399
chr9	108212340	108212436	E081	-17554
chr9	108213002	108213079	E081	-16911
chr9	108213593	108213946	E081	-16044
chr9	108214412	108214470	E081	-15520
chr9	108214552	108214715	E081	-15275
chr9	108214855	108214912	E081	-15078
chr9	108215052	108215102	E081	-14888
chr9	108221590	108221722	E081	-8268
chr9	108221746	108222017	E081	-7973
chr9	108222053	108222390	E081	-7600
chr9	108224156	108224221	E081	-5769
chr9	108224284	108224453	E081	-5537
chr9	108180672	108181782	E082	-48208
chr9	108181810	108181969	E082	-48021
chr9	108182176	108183027	E082	-46963
chr9	108213002	108213079	E082	-16911
chr9	108213593	108213946	E082	-16044
chr9	108214272	108214389	E082	-15601
chr9	108214412	108214470	E082	-15520
chr9	108214552	108214715	E082	-15275

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr9	108209679	108211627	E067	-18363
chr9	108209679	108211627	E068	-18363
chr9	108211629	108211662	E068	-18328
chr9	108209679	108211627	E069	-18363
chr9	108209679	108211627	E070	-18363
chr9	108211629	108211662	E070	-18328
chr9	108211749	108211824	E070	-18166
chr9	108209679	108211627	E071	-18363
chr9	108209679	108211627	E072	-18363
chr9	108209679	108211627	E073	-18363
chr9	108209679	108211627	E074	-18363
chr9	108209679	108211627	E081	-18363
chr9	108211629	108211662	E081	-18328
chr9	108211749	108211824	E081	-18166
chr9	108209679	108211627	E082	-18363
chr9	108211629	108211662	E082	-18328
chr9	108211749	108211824	E082	-18166