rs4807045

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SAFB2 : Intron Variant
SAFB : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0012 (366/29984,GnomAD)
C=0010 (316/29118,TOPMED)
C=0010 (51/5008,1000G)
C=0014 (54/3854,ALSPAC)
C=0010 (38/3708,TWINSUK)

Position: chr19:5621914 (GRCh38.p7) (19p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 376 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.5621914T>C
GRCh37.p13 chr 19	NC_000019.9:g.5621925T>C

Gene: SAFB2, scaffold attachment factor B2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SAFB2 transcript	NM_014649.2:c.	N/A	Intron Variant
SAFB2 transcript variant X1	XM_011528449.2:c.	N/A	Intron Variant
SAFB2 transcript variant X4	XM_017027522.1:c.	N/A	Intron Variant
SAFB2 transcript variant X5	XM_011528450.2:c.	N/A	Genic Upstream Transcript Variant
SAFB2 transcript variant X2	XM_017027520.1:c.	N/A	Genic Upstream Transcript Variant
SAFB2 transcript variant X3	XM_017027521.1:c.	N/A	Genic Upstream Transcript Variant

Gene: SAFB, scaffold attachment factor B(plus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
SAFB transcript variant 1	NM_001201338.1:c.	N/A	Upstream Transcript Variant
SAFB transcript variant 2	NM_001201339.1:c.	N/A	Upstream Transcript Variant
SAFB transcript variant 4	NM_001201340.1:c.	N/A	Upstream Transcript Variant
SAFB transcript variant 5	NM_001320571.1:c.	N/A	Upstream Transcript Variant
SAFB transcript variant 6	NM_001320572.1:c.	N/A	Upstream Transcript Variant
SAFB transcript variant 3	NM_002967.3:c.	N/A	Upstream Transcript Variant
SAFB transcript variant X1	XM_017027114.1:c.	N/A	Upstream Transcript Variant
SAFB transcript variant X2	XM_017027115.1:c.	N/A	Upstream Transcript Variant
SAFB transcript variant X3	XM_017027116.1:c.	N/A	Upstream Transcript Variant
SAFB transcript variant X4	XM_017027117.1:c.	N/A	Upstream Transcript Variant
SAFB transcript variant X5	XM_017027118.1:c.	N/A	Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=1.000	C=0.000
1000Genomes	American	Sub	694	T=0.990	C=0.010
1000Genomes	East Asian	Sub	1008	T=0.977	C=0.023
1000Genomes	Europe	Sub	1006	T=0.984	C=0.016
1000Genomes	Global	Study-wide	5008	T=0.990	C=0.010
1000Genomes	South Asian	Sub	978	T=0.990	C=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.986	C=0.014
The Genome Aggregation Database	African	Sub	8734	T=0.997	C=0.003
The Genome Aggregation Database	American	Sub	838	T=0.980	C=0.020
The Genome Aggregation Database	East Asian	Sub	1620	T=0.973	C=0.027
The Genome Aggregation Database	Europe	Sub	18490	T=0.985	C=0.015
The Genome Aggregation Database	Global	Study-wide	29984	T=0.987	C=0.012
The Genome Aggregation Database	Other	Sub	302	T=1.000	C=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.989	C=0.010
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.990	C=0.010

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

P-Value

SNP ID	p-value	Traits	Study
rs4807045	0.00091	alcohol dependence	20201924

eQTL of rs4807045 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 rs4807045 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 )
chr19	5577698	5578872	E067	-43053
chr19	5585165	5585231	E067	-36694
chr19	5585247	5586973	E067	-34952
chr19	5588144	5588208	E067	-33717
chr19	5588299	5588358	E067	-33567
chr19	5588425	5588548	E067	-33377
chr19	5588628	5588709	E067	-33216
chr19	5588775	5588965	E067	-32960
chr19	5588987	5589126	E067	-32799
chr19	5589173	5589341	E067	-32584
chr19	5589384	5589424	E067	-32501
chr19	5589532	5589606	E067	-32319
chr19	5589756	5589870	E067	-32055
chr19	5589973	5590120	E067	-31805
chr19	5617092	5617508	E067	-4417
chr19	5617699	5617786	E067	-4139
chr19	5618438	5618607	E067	-3318
chr19	5618979	5619110	E067	-2815
chr19	5619445	5619495	E067	-2430
chr19	5619688	5619732	E067	-2193
chr19	5619976	5620212	E067	-1713
chr19	5620541	5620699	E067	-1226
chr19	5625614	5625733	E067	3689
chr19	5625791	5625958	E067	3866
chr19	5626081	5626180	E067	4156
chr19	5626257	5626345	E067	4332
chr19	5626415	5626561	E067	4490
chr19	5626647	5626710	E067	4722
chr19	5626714	5626914	E067	4789
chr19	5626976	5627144	E067	5051
chr19	5627189	5627255	E067	5264
chr19	5627275	5627315	E067	5350
chr19	5627378	5627440	E067	5453
chr19	5627572	5627882	E067	5647
chr19	5630199	5630312	E067	8274
chr19	5631171	5631309	E067	9246
chr19	5631422	5631462	E067	9497
chr19	5631549	5632270	E067	9624
chr19	5632326	5632376	E067	10401
chr19	5632389	5632623	E067	10464
chr19	5632806	5633033	E067	10881
chr19	5633177	5633217	E067	11252
chr19	5633262	5633531	E067	11337
chr19	5637808	5637864	E067	15883
chr19	5637930	5638001	E067	16005
chr19	5638139	5638223	E067	16214
chr19	5650069	5650112	E067	28144
chr19	5585165	5585231	E068	-36694
chr19	5585247	5586973	E068	-34952
chr19	5587021	5587071	E068	-34854
chr19	5587201	5587255	E068	-34670
chr19	5587355	5587413	E068	-34512
chr19	5587451	5587529	E068	-34396
chr19	5587622	5587710	E068	-34215
chr19	5587773	5587909	E068	-34016
chr19	5588144	5588208	E068	-33717
chr19	5588299	5588358	E068	-33567
chr19	5588425	5588548	E068	-33377
chr19	5588628	5588709	E068	-33216
chr19	5588775	5588965	E068	-32960
chr19	5605596	5605749	E068	-16176
chr19	5605818	5605868	E068	-16057
chr19	5605952	5605992	E068	-15933
chr19	5617699	5617786	E068	-4139
chr19	5618438	5618607	E068	-3318
chr19	5618979	5619110	E068	-2815
chr19	5619174	5619258	E068	-2667
chr19	5619302	5619376	E068	-2549
chr19	5619445	5619495	E068	-2430
chr19	5619688	5619732	E068	-2193
chr19	5619976	5620212	E068	-1713
chr19	5626257	5626345	E068	4332
chr19	5626415	5626561	E068	4490
chr19	5626647	5626710	E068	4722
chr19	5626714	5626914	E068	4789
chr19	5626976	5627144	E068	5051
chr19	5627189	5627255	E068	5264
chr19	5627275	5627315	E068	5350
chr19	5627378	5627440	E068	5453
chr19	5627572	5627882	E068	5647
chr19	5629298	5629416	E068	7373
chr19	5629517	5629557	E068	7592
chr19	5629722	5629762	E068	7797
chr19	5629940	5630024	E068	8015
chr19	5630199	5630312	E068	8274
chr19	5631422	5631462	E068	9497
chr19	5631549	5632270	E068	9624
chr19	5632326	5632376	E068	10401
chr19	5632389	5632623	E068	10464
chr19	5644837	5644888	E068	22912
chr19	5645029	5645103	E068	23104
chr19	5585165	5585231	E069	-36694
chr19	5585247	5586973	E069	-34952
chr19	5587021	5587071	E069	-34854
chr19	5587201	5587255	E069	-34670
chr19	5587355	5587413	E069	-34512
chr19	5587451	5587529	E069	-34396
chr19	5587622	5587710	E069	-34215
chr19	5587773	5587909	E069	-34016
chr19	5588144	5588208	E069	-33717
chr19	5588299	5588358	E069	-33567
chr19	5588425	5588548	E069	-33377
chr19	5588628	5588709	E069	-33216
chr19	5588775	5588965	E069	-32960
chr19	5588987	5589126	E069	-32799
chr19	5589173	5589341	E069	-32584
chr19	5589384	5589424	E069	-32501
chr19	5589532	5589606	E069	-32319
chr19	5589756	5589870	E069	-32055
chr19	5595382	5595452	E069	-26473
chr19	5595535	5595588	E069	-26337
chr19	5618979	5619110	E069	-2815
chr19	5619174	5619258	E069	-2667
chr19	5619302	5619376	E069	-2549
chr19	5619445	5619495	E069	-2430
chr19	5619688	5619732	E069	-2193
chr19	5619976	5620212	E069	-1713
chr19	5620541	5620699	E069	-1226
chr19	5625791	5625958	E069	3866
chr19	5626081	5626180	E069	4156
chr19	5626257	5626345	E069	4332
chr19	5626415	5626561	E069	4490
chr19	5626647	5626710	E069	4722
chr19	5626714	5626914	E069	4789
chr19	5626976	5627144	E069	5051
chr19	5627189	5627255	E069	5264
chr19	5627275	5627315	E069	5350
chr19	5627378	5627440	E069	5453
chr19	5627572	5627882	E069	5647
chr19	5628352	5628409	E069	6427
chr19	5628543	5628813	E069	6618
chr19	5628955	5629267	E069	7030
chr19	5629298	5629416	E069	7373
chr19	5629517	5629557	E069	7592
chr19	5629722	5629762	E069	7797
chr19	5629940	5630024	E069	8015
chr19	5630199	5630312	E069	8274
chr19	5631171	5631309	E069	9246
chr19	5631422	5631462	E069	9497
chr19	5631549	5632270	E069	9624
chr19	5632326	5632376	E069	10401
chr19	5632389	5632623	E069	10464
chr19	5632806	5633033	E069	10881
chr19	5633177	5633217	E069	11252
chr19	5633262	5633531	E069	11337
chr19	5637386	5637457	E069	15461
chr19	5637808	5637864	E069	15883
chr19	5637930	5638001	E069	16005
chr19	5585247	5586973	E070	-34952
chr19	5587021	5587071	E070	-34854
chr19	5619302	5619376	E070	-2549
chr19	5619976	5620212	E070	-1713
chr19	5626257	5626345	E070	4332
chr19	5626415	5626561	E070	4490
chr19	5626647	5626710	E070	4722
chr19	5626714	5626914	E070	4789
chr19	5626976	5627144	E070	5051
chr19	5627189	5627255	E070	5264
chr19	5627275	5627315	E070	5350
chr19	5627378	5627440	E070	5453
chr19	5635636	5635701	E070	13711
chr19	5635762	5635837	E070	13837
chr19	5585165	5585231	E071	-36694
chr19	5585247	5586973	E071	-34952
chr19	5587021	5587071	E071	-34854
chr19	5587201	5587255	E071	-34670
chr19	5587355	5587413	E071	-34512
chr19	5587451	5587529	E071	-34396
chr19	5587622	5587710	E071	-34215
chr19	5587773	5587909	E071	-34016
chr19	5588144	5588208	E071	-33717
chr19	5588299	5588358	E071	-33567
chr19	5588425	5588548	E071	-33377
chr19	5588628	5588709	E071	-33216
chr19	5588775	5588965	E071	-32960
chr19	5588987	5589126	E071	-32799
chr19	5589173	5589341	E071	-32584
chr19	5589384	5589424	E071	-32501
chr19	5589532	5589606	E071	-32319
chr19	5589756	5589870	E071	-32055
chr19	5595162	5595372	E071	-26553
chr19	5595382	5595452	E071	-26473
chr19	5595535	5595588	E071	-26337
chr19	5605596	5605749	E071	-16176
chr19	5605818	5605868	E071	-16057
chr19	5605952	5605992	E071	-15933
chr19	5606004	5606055	E071	-15870
chr19	5618438	5618607	E071	-3318
chr19	5618979	5619110	E071	-2815
chr19	5619174	5619258	E071	-2667
chr19	5619302	5619376	E071	-2549
chr19	5619445	5619495	E071	-2430
chr19	5619688	5619732	E071	-2193
chr19	5619976	5620212	E071	-1713
chr19	5620541	5620699	E071	-1226
chr19	5626081	5626180	E071	4156
chr19	5626257	5626345	E071	4332
chr19	5626415	5626561	E071	4490
chr19	5626647	5626710	E071	4722
chr19	5626714	5626914	E071	4789
chr19	5626976	5627144	E071	5051
chr19	5627189	5627255	E071	5264
chr19	5627275	5627315	E071	5350
chr19	5627378	5627440	E071	5453
chr19	5627572	5627882	E071	5647
chr19	5628352	5628409	E071	6427
chr19	5628543	5628813	E071	6618
chr19	5628955	5629267	E071	7030
chr19	5629298	5629416	E071	7373
chr19	5629517	5629557	E071	7592
chr19	5629722	5629762	E071	7797
chr19	5629940	5630024	E071	8015
chr19	5630199	5630312	E071	8274
chr19	5630521	5630565	E071	8596
chr19	5630740	5630784	E071	8815
chr19	5631171	5631309	E071	9246
chr19	5631422	5631462	E071	9497
chr19	5631549	5632270	E071	9624
chr19	5632326	5632376	E071	10401
chr19	5632389	5632623	E071	10464
chr19	5637808	5637864	E071	15883
chr19	5637930	5638001	E071	16005
chr19	5644175	5644350	E071	22250
chr19	5644837	5644888	E071	22912
chr19	5585247	5586973	E072	-34952
chr19	5587021	5587071	E072	-34854
chr19	5587201	5587255	E072	-34670
chr19	5587355	5587413	E072	-34512
chr19	5587451	5587529	E072	-34396
chr19	5587622	5587710	E072	-34215
chr19	5587773	5587909	E072	-34016
chr19	5588144	5588208	E072	-33717
chr19	5588299	5588358	E072	-33567
chr19	5588425	5588548	E072	-33377
chr19	5588628	5588709	E072	-33216
chr19	5588775	5588965	E072	-32960
chr19	5588987	5589126	E072	-32799
chr19	5589173	5589341	E072	-32584
chr19	5589384	5589424	E072	-32501
chr19	5589532	5589606	E072	-32319
chr19	5617699	5617786	E072	-4139
chr19	5618438	5618607	E072	-3318
chr19	5618979	5619110	E072	-2815
chr19	5619174	5619258	E072	-2667
chr19	5619302	5619376	E072	-2549
chr19	5619445	5619495	E072	-2430
chr19	5619688	5619732	E072	-2193
chr19	5619976	5620212	E072	-1713
chr19	5620541	5620699	E072	-1226
chr19	5626415	5626561	E072	4490
chr19	5626647	5626710	E072	4722
chr19	5626714	5626914	E072	4789
chr19	5626976	5627144	E072	5051
chr19	5627189	5627255	E072	5264
chr19	5627275	5627315	E072	5350
chr19	5627378	5627440	E072	5453
chr19	5627572	5627882	E072	5647
chr19	5628955	5629267	E072	7030
chr19	5629298	5629416	E072	7373
chr19	5629517	5629557	E072	7592
chr19	5629722	5629762	E072	7797
chr19	5629940	5630024	E072	8015
chr19	5630199	5630312	E072	8274
chr19	5631549	5632270	E072	9624
chr19	5632326	5632376	E072	10401
chr19	5632389	5632623	E072	10464
chr19	5632806	5633033	E072	10881
chr19	5635202	5635252	E072	13277
chr19	5635405	5635518	E072	13480
chr19	5635636	5635701	E072	13711
chr19	5635762	5635837	E072	13837
chr19	5636020	5636213	E072	14095
chr19	5652320	5652375	E072	30395
chr19	5652420	5652646	E072	30495
chr19	5577698	5578872	E073	-43053
chr19	5585165	5585231	E073	-36694
chr19	5585247	5586973	E073	-34952
chr19	5587021	5587071	E073	-34854
chr19	5587201	5587255	E073	-34670
chr19	5587355	5587413	E073	-34512
chr19	5587451	5587529	E073	-34396
chr19	5587622	5587710	E073	-34215
chr19	5587773	5587909	E073	-34016
chr19	5588144	5588208	E073	-33717
chr19	5588299	5588358	E073	-33567
chr19	5588425	5588548	E073	-33377
chr19	5588628	5588709	E073	-33216
chr19	5588775	5588965	E073	-32960
chr19	5588987	5589126	E073	-32799
chr19	5589173	5589341	E073	-32584
chr19	5589384	5589424	E073	-32501
chr19	5589532	5589606	E073	-32319
chr19	5589756	5589870	E073	-32055
chr19	5589973	5590120	E073	-31805
chr19	5590243	5590372	E073	-31553
chr19	5590413	5590463	E073	-31462
chr19	5590865	5590963	E073	-30962
chr19	5590996	5591091	E073	-30834
chr19	5591109	5591220	E073	-30705
chr19	5620541	5620699	E073	-1226
chr19	5626081	5626180	E073	4156
chr19	5626257	5626345	E073	4332
chr19	5627378	5627440	E073	5453
chr19	5627572	5627882	E073	5647
chr19	5628955	5629267	E073	7030
chr19	5629298	5629416	E073	7373
chr19	5629517	5629557	E073	7592
chr19	5629722	5629762	E073	7797
chr19	5630199	5630312	E073	8274
chr19	5631549	5632270	E073	9624
chr19	5632326	5632376	E073	10401
chr19	5632389	5632623	E073	10464
chr19	5632806	5633033	E073	10881
chr19	5633177	5633217	E073	11252
chr19	5637808	5637864	E073	15883
chr19	5585165	5585231	E074	-36694
chr19	5585247	5586973	E074	-34952
chr19	5587021	5587071	E074	-34854
chr19	5587201	5587255	E074	-34670
chr19	5587355	5587413	E074	-34512
chr19	5587451	5587529	E074	-34396
chr19	5587622	5587710	E074	-34215
chr19	5587773	5587909	E074	-34016
chr19	5588144	5588208	E074	-33717
chr19	5588299	5588358	E074	-33567
chr19	5588425	5588548	E074	-33377
chr19	5605596	5605749	E074	-16176
chr19	5605818	5605868	E074	-16057
chr19	5605952	5605992	E074	-15933
chr19	5606004	5606055	E074	-15870
chr19	5618979	5619110	E074	-2815
chr19	5619174	5619258	E074	-2667
chr19	5619302	5619376	E074	-2549
chr19	5619445	5619495	E074	-2430
chr19	5625457	5625518	E074	3532
chr19	5625614	5625733	E074	3689
chr19	5625791	5625958	E074	3866
chr19	5626081	5626180	E074	4156
chr19	5626257	5626345	E074	4332
chr19	5626415	5626561	E074	4490
chr19	5626647	5626710	E074	4722
chr19	5626714	5626914	E074	4789
chr19	5626976	5627144	E074	5051
chr19	5627189	5627255	E074	5264
chr19	5627275	5627315	E074	5350
chr19	5627378	5627440	E074	5453
chr19	5627572	5627882	E074	5647
chr19	5628352	5628409	E074	6427
chr19	5628543	5628813	E074	6618
chr19	5628955	5629267	E074	7030
chr19	5629298	5629416	E074	7373
chr19	5629517	5629557	E074	7592
chr19	5629722	5629762	E074	7797
chr19	5630521	5630565	E074	8596
chr19	5630740	5630784	E074	8815
chr19	5631171	5631309	E074	9246
chr19	5631422	5631462	E074	9497
chr19	5631549	5632270	E074	9624
chr19	5632326	5632376	E074	10401
chr19	5632389	5632623	E074	10464
chr19	5632806	5633033	E074	10881
chr19	5633177	5633217	E074	11252
chr19	5577698	5578872	E081	-43053
chr19	5585247	5586973	E081	-34952
chr19	5620541	5620699	E081	-1226
chr19	5620914	5621300	E081	-625
chr19	5626081	5626180	E081	4156
chr19	5626257	5626345	E081	4332
chr19	5626415	5626561	E081	4490
chr19	5626647	5626710	E081	4722
chr19	5626714	5626914	E081	4789
chr19	5626976	5627144	E081	5051
chr19	5577698	5578872	E082	-43053
chr19	5585247	5586973	E082	-34952
chr19	5619976	5620212	E082	-1713
chr19	5620541	5620699	E082	-1226

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region
chr19	5621331	5624668	E067
chr19	5621331	5624668	E068
chr19	5621331	5624668	E069
chr19	5621331	5624668	E070
chr19	5621331	5624668	E071
chr19	5621331	5624668	E072
chr19	5621331	5624668	E073
chr19	5621331	5624668	E074
chr19	5621331	5624668	E081
chr19	5621331	5624668	E082