rs3753563

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

RABGAP1L : Intron Variant
LOC101928696 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0258 (7736/29938,GnomAD)
T==0225 (6569/29118,TOPMED)
T==0278 (1393/5008,1000G)
T==0334 (1287/3854,ALSPAC)
T==0353 (1310/3708,TWINSUK)

Position: chr1:174954209 (GRCh38.p7) (1q25.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 162 Enhancers around

Promoter: 24 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.174954209T>C
GRCh37.p13 chr 1	NC_000001.10:g.174923346T>C

Gene: RABGAP1L, RAB GTPase activating protein 1-like(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RABGAP1L transcript variant 2	NM_001035230.2:c.	N/A	Intron Variant
RABGAP1L transcript variant 3	NM_001243763.1:c.	N/A	Intron Variant
RABGAP1L transcript variant 4	NM_001243765.1:c.	N/A	Intron Variant
RABGAP1L transcript variant 1	NM_014857.4:c.	N/A	Intron Variant
RABGAP1L transcript variant 5	NM_001243764.1:c.	N/A	Genic Upstream Transcript Variant
RABGAP1L transcript variant X1	XM_005245680.1:c.	N/A	Intron Variant
RABGAP1L transcript variant X3	XM_005245681.2:c.	N/A	Intron Variant
RABGAP1L transcript variant X4	XM_006711693.1:c.	N/A	Intron Variant
RABGAP1L transcript variant X2	XM_011510223.2:c.	N/A	Intron Variant
RABGAP1L transcript variant X7	XM_017002994.1:c.	N/A	Intron Variant
RABGAP1L transcript variant X8	XM_017002995.1:c.	N/A	Intron Variant
RABGAP1L transcript variant X8	XM_017002996.1:c.	N/A	Intron Variant
RABGAP1L transcript variant X9	XM_017002997.1:c.	N/A	Intron Variant
RABGAP1L transcript variant X11	XM_017002998.1:c.	N/A	Intron Variant
RABGAP1L transcript variant X12	XM_017002999.1:c.	N/A	Intron Variant
RABGAP1L transcript variant X5	XR_001737553.1:n.	N/A	Intron Variant
RABGAP1L transcript variant X6	XR_922004.1:n.	N/A	Intron Variant

Gene: LOC101928696, uncharacterized LOC101928696(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101928696 transcript	NR_121196.1:n.53A>G	A>G	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.019	C=0.981
1000Genomes	American	Sub	694	T=0.410	C=0.590
1000Genomes	East Asian	Sub	1008	T=0.398	C=0.602
1000Genomes	Europe	Sub	1006	T=0.341	C=0.659
1000Genomes	Global	Study-wide	5008	T=0.278	C=0.722
1000Genomes	South Asian	Sub	978	T=0.350	C=0.650
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.334	C=0.666
The Genome Aggregation Database	African	Sub	8720	T=0.068	C=0.932
The Genome Aggregation Database	American	Sub	838	T=0.460	C=0.540
The Genome Aggregation Database	East Asian	Sub	1614	T=0.362	C=0.638
The Genome Aggregation Database	Europe	Sub	18464	T=0.329	C=0.670
The Genome Aggregation Database	Global	Study-wide	29938	T=0.258	C=0.741
The Genome Aggregation Database	Other	Sub	302	T=0.270	C=0.730
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.225	C=0.774
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.353	C=0.647

PMID	Title	Author	Journal
21529783	A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.	Heath AC	Biol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs3753563	7.7E-05	alcoholism (heaviness of drinking)	21529783

eQTL of rs3753563 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 rs3753563 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	174897246	174897386	E067	-25960
chr1	174900538	174900965	E067	-22381
chr1	174911279	174911329	E067	-12017
chr1	174911343	174911433	E067	-11913
chr1	174911864	174911939	E067	-11407
chr1	174912054	174912340	E067	-11006
chr1	174912470	174912520	E067	-10826
chr1	174922416	174922935	E067	-411
chr1	174922973	174923634	E067	0
chr1	174923776	174924682	E067	430
chr1	174924689	174924761	E067	1343
chr1	174924827	174924900	E067	1481
chr1	174927005	174927087	E067	3659
chr1	174927334	174927379	E067	3988
chr1	174927797	174927857	E067	4451
chr1	174933362	174935576	E067	10016
chr1	174943907	174943996	E067	20561
chr1	174944154	174944253	E067	20808
chr1	174945454	174946402	E067	22108
chr1	174952264	174952735	E067	28918
chr1	174970961	174971021	E067	47615
chr1	174971194	174971269	E067	47848
chr1	174971298	174971361	E067	47952
chr1	174971530	174971632	E067	48184
chr1	174887096	174887136	E068	-36210
chr1	174897246	174897386	E068	-25960
chr1	174897509	174897617	E068	-25729
chr1	174897694	174897756	E068	-25590
chr1	174900538	174900965	E068	-22381
chr1	174911279	174911329	E068	-12017
chr1	174911343	174911433	E068	-11913
chr1	174912470	174912520	E068	-10826
chr1	174914901	174915074	E068	-8272
chr1	174922416	174922935	E068	-411
chr1	174922973	174923634	E068	0
chr1	174923776	174924682	E068	430
chr1	174927005	174927087	E068	3659
chr1	174927334	174927379	E068	3988
chr1	174927797	174927857	E068	4451
chr1	174933362	174935576	E068	10016
chr1	174935794	174935998	E068	12448
chr1	174940826	174940890	E068	17480
chr1	174941077	174941384	E068	17731
chr1	174944996	174945057	E068	21650
chr1	174970961	174971021	E068	47615
chr1	174900538	174900965	E069	-22381
chr1	174907554	174908183	E069	-15163
chr1	174911279	174911329	E069	-12017
chr1	174911343	174911433	E069	-11913
chr1	174911864	174911939	E069	-11407
chr1	174912054	174912340	E069	-11006
chr1	174912470	174912520	E069	-10826
chr1	174914901	174915074	E069	-8272
chr1	174915115	174915506	E069	-7840
chr1	174922416	174922935	E069	-411
chr1	174922973	174923634	E069	0
chr1	174923776	174924682	E069	430
chr1	174924689	174924761	E069	1343
chr1	174927005	174927087	E069	3659
chr1	174927334	174927379	E069	3988
chr1	174927797	174927857	E069	4451
chr1	174933362	174935576	E069	10016
chr1	174958725	174958772	E069	35379
chr1	174958823	174958906	E069	35477
chr1	174970961	174971021	E069	47615
chr1	174971791	174971876	E069	48445
chr1	174971897	174971958	E069	48551
chr1	174972162	174972241	E069	48816
chr1	174972636	174972680	E069	49290
chr1	174972719	174972870	E069	49373
chr1	174922973	174923634	E070	0
chr1	174897246	174897386	E071	-25960
chr1	174897509	174897617	E071	-25729
chr1	174897694	174897756	E071	-25590
chr1	174900538	174900965	E071	-22381
chr1	174901408	174901488	E071	-21858
chr1	174907554	174908183	E071	-15163
chr1	174911279	174911329	E071	-12017
chr1	174911343	174911433	E071	-11913
chr1	174911864	174911939	E071	-11407
chr1	174912054	174912340	E071	-11006
chr1	174912470	174912520	E071	-10826
chr1	174914901	174915074	E071	-8272
chr1	174915115	174915506	E071	-7840
chr1	174922416	174922935	E071	-411
chr1	174922973	174923634	E071	0
chr1	174923776	174924682	E071	430
chr1	174924689	174924761	E071	1343
chr1	174927005	174927087	E071	3659
chr1	174927334	174927379	E071	3988
chr1	174927797	174927857	E071	4451
chr1	174933362	174935576	E071	10016
chr1	174943907	174943996	E071	20561
chr1	174944154	174944253	E071	20808
chr1	174897509	174897617	E072	-25729
chr1	174900538	174900965	E072	-22381
chr1	174901408	174901488	E072	-21858
chr1	174907554	174908183	E072	-15163
chr1	174911279	174911329	E072	-12017
chr1	174911343	174911433	E072	-11913
chr1	174912054	174912340	E072	-11006
chr1	174912470	174912520	E072	-10826
chr1	174922416	174922935	E072	-411
chr1	174922973	174923634	E072	0
chr1	174923776	174924682	E072	430
chr1	174924689	174924761	E072	1343
chr1	174924827	174924900	E072	1481
chr1	174927797	174927857	E072	4451
chr1	174933362	174935576	E072	10016
chr1	174941077	174941384	E072	17731
chr1	174943907	174943996	E072	20561
chr1	174944154	174944253	E072	20808
chr1	174944649	174944703	E072	21303
chr1	174944996	174945057	E072	21650
chr1	174945454	174946402	E072	22108
chr1	174971530	174971632	E072	48184
chr1	174971791	174971876	E072	48445
chr1	174880828	174881085	E073	-42261
chr1	174911279	174911329	E073	-12017
chr1	174911343	174911433	E073	-11913
chr1	174911864	174911939	E073	-11407
chr1	174912054	174912340	E073	-11006
chr1	174912470	174912520	E073	-10826
chr1	174922416	174922935	E073	-411
chr1	174922973	174923634	E073	0
chr1	174933362	174935576	E073	10016
chr1	174943907	174943996	E073	20561
chr1	174944154	174944253	E073	20808
chr1	174944649	174944703	E073	21303
chr1	174944996	174945057	E073	21650
chr1	174971530	174971632	E073	48184
chr1	174971791	174971876	E073	48445
chr1	174971897	174971958	E073	48551
chr1	174972162	174972241	E073	48816
chr1	174972636	174972680	E073	49290
chr1	174972719	174972870	E073	49373
chr1	174897246	174897386	E074	-25960
chr1	174897509	174897617	E074	-25729
chr1	174897694	174897756	E074	-25590
chr1	174900538	174900965	E074	-22381
chr1	174901408	174901488	E074	-21858
chr1	174911279	174911329	E074	-12017
chr1	174911343	174911433	E074	-11913
chr1	174911864	174911939	E074	-11407
chr1	174912054	174912340	E074	-11006
chr1	174912470	174912520	E074	-10826
chr1	174922416	174922935	E074	-411
chr1	174922973	174923634	E074	0
chr1	174923776	174924682	E074	430
chr1	174927005	174927087	E074	3659
chr1	174927334	174927379	E074	3988
chr1	174927797	174927857	E074	4451
chr1	174933362	174935576	E074	10016
chr1	174935794	174935998	E074	12448
chr1	174958725	174958772	E074	35379
chr1	174958823	174958906	E074	35477
chr1	174970961	174971021	E074	47615
chr1	174881677	174881821	E081	-41525
chr1	174884240	174884357	E081	-38989
chr1	174970961	174971021	E081	47615
chr1	174880828	174881085	E082	-42261
chr1	174923776	174924682	E082	430

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	174959538	174960006	E067	36192
chr1	174960023	174960150	E067	36677
chr1	174967592	174970365	E067	44246
chr1	174959538	174960006	E068	36192
chr1	174960023	174960150	E068	36677
chr1	174967592	174970365	E068	44246
chr1	174959538	174960006	E069	36192
chr1	174960023	174960150	E069	36677
chr1	174967592	174970365	E069	44246
chr1	174967592	174970365	E070	44246
chr1	174959538	174960006	E071	36192
chr1	174960023	174960150	E071	36677
chr1	174967592	174970365	E071	44246
chr1	174959538	174960006	E072	36192
chr1	174960023	174960150	E072	36677
chr1	174967592	174970365	E072	44246
chr1	174959538	174960006	E073	36192
chr1	174960023	174960150	E073	36677
chr1	174967592	174970365	E073	44246
chr1	174959538	174960006	E074	36192
chr1	174960023	174960150	E074	36677
chr1	174967592	174970365	E074	44246
chr1	174967592	174970365	E081	44246
chr1	174967592	174970365	E082	44246