rs6537803

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC105378893 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0329 (9864/29916,GnomAD)
A=0364 (10620/29118,TOPMED)
A=0345 (1727/5008,1000G)
A=0242 (932/3854,ALSPAC)
A=0239 (886/3708,TWINSUK)

Position: chr1:109520918 (GRCh38.p7) (1p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 340 Enhancers around

Promoter: 66 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.109520918G>A
GRCh37.p13 chr 1	NC_000001.10:g.110063540G>A

Gene: LOC105378893, uncharacterized LOC105378893(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378893 transcript	XR_001738179.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.435	A=0.565
1000Genomes	American	Sub	694	G=0.820	A=0.180
1000Genomes	East Asian	Sub	1008	G=0.723	A=0.277
1000Genomes	Europe	Sub	1006	G=0.767	A=0.233
1000Genomes	Global	Study-wide	5008	G=0.655	A=0.345
1000Genomes	South Asian	Sub	978	G=0.650	A=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.758	A=0.242
The Genome Aggregation Database	African	Sub	8708	G=0.475	A=0.525
The Genome Aggregation Database	American	Sub	836	G=0.830	A=0.170
The Genome Aggregation Database	East Asian	Sub	1610	G=0.747	A=0.253
The Genome Aggregation Database	Europe	Sub	18460	G=0.747	A=0.253
The Genome Aggregation Database	Global	Study-wide	29916	G=0.670	A=0.329
The Genome Aggregation Database	Other	Sub	302	G=0.770	A=0.230
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.635	A=0.364
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.761	A=0.239

PMID	Title	Author	Journal
22072270	Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms.	Wang KS	J Neural Transm (Vienna)

P-Value

SNP ID	p-value	Traits	Study
rs6537803	7.54E-05	alcohol withdrawal symptoms	22072270

eQTL of rs6537803 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:110063540	SYPL2	ENSG00000143028.7	G>A	1.5811e-10	54360	Cerebellum
Chr1:110063540	AMIGO1	ENSG00000181754.6	G>A	3.6792e-3	11180	Cerebellum

meQTL of rs6537803 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	110028135	110028380	E067	-35160
chr1	110035747	110035946	E067	-27594
chr1	110035968	110036049	E067	-27491
chr1	110036059	110036099	E067	-27441
chr1	110036107	110036179	E067	-27361
chr1	110040305	110040378	E067	-23162
chr1	110040500	110041442	E067	-22098
chr1	110041569	110041630	E067	-21910
chr1	110041744	110041979	E067	-21561
chr1	110042000	110042040	E067	-21500
chr1	110042286	110042922	E067	-20618
chr1	110042923	110043019	E067	-20521
chr1	110043169	110043215	E067	-20325
chr1	110043229	110043273	E067	-20267
chr1	110043289	110043329	E067	-20211
chr1	110043413	110043556	E067	-19984
chr1	110043610	110043988	E067	-19552
chr1	110050718	110050768	E067	-12772
chr1	110051027	110051117	E067	-12423
chr1	110053049	110053213	E067	-10327
chr1	110053266	110053341	E067	-10199
chr1	110072201	110072305	E067	8661
chr1	110072314	110072386	E067	8774
chr1	110072485	110073884	E067	8945
chr1	110073981	110074056	E067	10441
chr1	110074119	110074176	E067	10579
chr1	110074250	110074300	E067	10710
chr1	110074338	110074451	E067	10798
chr1	110074527	110074725	E067	10987
chr1	110078077	110078174	E067	14537
chr1	110078199	110078303	E067	14659
chr1	110078560	110079130	E067	15020
chr1	110079196	110079338	E067	15656
chr1	110105884	110105949	E067	42344
chr1	110105989	110106400	E067	42449
chr1	110106523	110106583	E067	42983
chr1	110106587	110106647	E067	43047
chr1	110110588	110110792	E067	47048
chr1	110110888	110110939	E067	47348
chr1	110111719	110111819	E067	48179
chr1	110111872	110111952	E067	48332
chr1	110112108	110112184	E067	48568
chr1	110113013	110113521	E067	49473
chr1	110035747	110035946	E068	-27594
chr1	110035968	110036049	E068	-27491
chr1	110036059	110036099	E068	-27441
chr1	110036107	110036179	E068	-27361
chr1	110040305	110040378	E068	-23162
chr1	110040500	110041442	E068	-22098
chr1	110041569	110041630	E068	-21910
chr1	110041744	110041979	E068	-21561
chr1	110042286	110042922	E068	-20618
chr1	110042923	110043019	E068	-20521
chr1	110043169	110043215	E068	-20325
chr1	110043229	110043273	E068	-20267
chr1	110043289	110043329	E068	-20211
chr1	110043413	110043556	E068	-19984
chr1	110043610	110043988	E068	-19552
chr1	110053266	110053341	E068	-10199
chr1	110072201	110072305	E068	8661
chr1	110072314	110072386	E068	8774
chr1	110072485	110073884	E068	8945
chr1	110073981	110074056	E068	10441
chr1	110074119	110074176	E068	10579
chr1	110074250	110074300	E068	10710
chr1	110074338	110074451	E068	10798
chr1	110074527	110074725	E068	10987
chr1	110078077	110078174	E068	14537
chr1	110078199	110078303	E068	14659
chr1	110078560	110079130	E068	15020
chr1	110079196	110079338	E068	15656
chr1	110105884	110105949	E068	42344
chr1	110105989	110106400	E068	42449
chr1	110110588	110110792	E068	47048
chr1	110110888	110110939	E068	47348
chr1	110111719	110111819	E068	48179
chr1	110111872	110111952	E068	48332
chr1	110112108	110112184	E068	48568
chr1	110028454	110028510	E069	-35030
chr1	110035747	110035946	E069	-27594
chr1	110035968	110036049	E069	-27491
chr1	110036059	110036099	E069	-27441
chr1	110036107	110036179	E069	-27361
chr1	110038933	110038984	E069	-24556
chr1	110039414	110039464	E069	-24076
chr1	110040305	110040378	E069	-23162
chr1	110050718	110050768	E069	-12772
chr1	110051027	110051117	E069	-12423
chr1	110053266	110053341	E069	-10199
chr1	110072201	110072305	E069	8661
chr1	110072314	110072386	E069	8774
chr1	110072485	110073884	E069	8945
chr1	110073981	110074056	E069	10441
chr1	110074119	110074176	E069	10579
chr1	110074250	110074300	E069	10710
chr1	110074338	110074451	E069	10798
chr1	110074527	110074725	E069	10987
chr1	110078199	110078303	E069	14659
chr1	110078560	110079130	E069	15020
chr1	110079196	110079338	E069	15656
chr1	110082405	110082583	E069	18865
chr1	110105884	110105949	E069	42344
chr1	110105989	110106400	E069	42449
chr1	110106523	110106583	E069	42983
chr1	110106587	110106647	E069	43047
chr1	110106772	110106844	E069	43232
chr1	110106951	110107356	E069	43411
chr1	110109683	110109891	E069	46143
chr1	110109939	110109979	E069	46399
chr1	110110588	110110792	E069	47048
chr1	110028454	110028510	E070	-35030
chr1	110028685	110028751	E070	-34789
chr1	110028806	110028860	E070	-34680
chr1	110030010	110030131	E070	-33409
chr1	110030275	110030353	E070	-33187
chr1	110030393	110030443	E070	-33097
chr1	110030502	110030622	E070	-32918
chr1	110035747	110035946	E070	-27594
chr1	110035968	110036049	E070	-27491
chr1	110036059	110036099	E070	-27441
chr1	110036107	110036179	E070	-27361
chr1	110040305	110040378	E070	-23162
chr1	110040500	110041442	E070	-22098
chr1	110041569	110041630	E070	-21910
chr1	110041744	110041979	E070	-21561
chr1	110042000	110042040	E070	-21500
chr1	110042286	110042922	E070	-20618
chr1	110042923	110043019	E070	-20521
chr1	110043169	110043215	E070	-20325
chr1	110043229	110043273	E070	-20267
chr1	110043289	110043329	E070	-20211
chr1	110043413	110043556	E070	-19984
chr1	110043610	110043988	E070	-19552
chr1	110053266	110053341	E070	-10199
chr1	110063562	110063940	E070	22
chr1	110064419	110064567	E070	879
chr1	110072201	110072305	E070	8661
chr1	110072314	110072386	E070	8774
chr1	110072485	110073884	E070	8945
chr1	110073981	110074056	E070	10441
chr1	110074119	110074176	E070	10579
chr1	110074250	110074300	E070	10710
chr1	110074338	110074451	E070	10798
chr1	110074527	110074725	E070	10987
chr1	110078077	110078174	E070	14537
chr1	110078199	110078303	E070	14659
chr1	110078560	110079130	E070	15020
chr1	110033101	110033686	E071	-29854
chr1	110033689	110033979	E071	-29561
chr1	110035968	110036049	E071	-27491
chr1	110036059	110036099	E071	-27441
chr1	110036107	110036179	E071	-27361
chr1	110041569	110041630	E071	-21910
chr1	110041744	110041979	E071	-21561
chr1	110042286	110042922	E071	-20618
chr1	110042923	110043019	E071	-20521
chr1	110043169	110043215	E071	-20325
chr1	110043229	110043273	E071	-20267
chr1	110043289	110043329	E071	-20211
chr1	110043413	110043556	E071	-19984
chr1	110043610	110043988	E071	-19552
chr1	110053049	110053213	E071	-10327
chr1	110072201	110072305	E071	8661
chr1	110072314	110072386	E071	8774
chr1	110072485	110073884	E071	8945
chr1	110073981	110074056	E071	10441
chr1	110074119	110074176	E071	10579
chr1	110074250	110074300	E071	10710
chr1	110074338	110074451	E071	10798
chr1	110074527	110074725	E071	10987
chr1	110078077	110078174	E071	14537
chr1	110078199	110078303	E071	14659
chr1	110078560	110079130	E071	15020
chr1	110079196	110079338	E071	15656
chr1	110082405	110082583	E071	18865
chr1	110105884	110105949	E071	42344
chr1	110105989	110106400	E071	42449
chr1	110106523	110106583	E071	42983
chr1	110106587	110106647	E071	43047
chr1	110106772	110106844	E071	43232
chr1	110106951	110107356	E071	43411
chr1	110109683	110109891	E071	46143
chr1	110109939	110109979	E071	46399
chr1	110110588	110110792	E071	47048
chr1	110110888	110110939	E071	47348
chr1	110111719	110111819	E071	48179
chr1	110111872	110111952	E071	48332
chr1	110112108	110112184	E071	48568
chr1	110028014	110028058	E072	-35482
chr1	110028135	110028380	E072	-35160
chr1	110033101	110033686	E072	-29854
chr1	110035968	110036049	E072	-27491
chr1	110036059	110036099	E072	-27441
chr1	110036107	110036179	E072	-27361
chr1	110038933	110038984	E072	-24556
chr1	110040305	110040378	E072	-23162
chr1	110040500	110041442	E072	-22098
chr1	110041569	110041630	E072	-21910
chr1	110041744	110041979	E072	-21561
chr1	110042000	110042040	E072	-21500
chr1	110042286	110042922	E072	-20618
chr1	110042923	110043019	E072	-20521
chr1	110043169	110043215	E072	-20325
chr1	110043229	110043273	E072	-20267
chr1	110043289	110043329	E072	-20211
chr1	110043413	110043556	E072	-19984
chr1	110043610	110043988	E072	-19552
chr1	110050718	110050768	E072	-12772
chr1	110051027	110051117	E072	-12423
chr1	110070849	110070919	E072	7309
chr1	110072201	110072305	E072	8661
chr1	110072314	110072386	E072	8774
chr1	110072485	110073884	E072	8945
chr1	110073981	110074056	E072	10441
chr1	110074119	110074176	E072	10579
chr1	110074250	110074300	E072	10710
chr1	110074338	110074451	E072	10798
chr1	110078199	110078303	E072	14659
chr1	110078560	110079130	E072	15020
chr1	110105884	110105949	E072	42344
chr1	110105989	110106400	E072	42449
chr1	110106523	110106583	E072	42983
chr1	110106587	110106647	E072	43047
chr1	110106772	110106844	E072	43232
chr1	110106951	110107356	E072	43411
chr1	110110588	110110792	E072	47048
chr1	110028014	110028058	E073	-35482
chr1	110028135	110028380	E073	-35160
chr1	110033101	110033686	E073	-29854
chr1	110033689	110033979	E073	-29561
chr1	110035603	110035704	E073	-27836
chr1	110040305	110040378	E073	-23162
chr1	110040500	110041442	E073	-22098
chr1	110041569	110041630	E073	-21910
chr1	110041744	110041979	E073	-21561
chr1	110042000	110042040	E073	-21500
chr1	110042286	110042922	E073	-20618
chr1	110042923	110043019	E073	-20521
chr1	110043169	110043215	E073	-20325
chr1	110043229	110043273	E073	-20267
chr1	110043289	110043329	E073	-20211
chr1	110043413	110043556	E073	-19984
chr1	110043610	110043988	E073	-19552
chr1	110064225	110064413	E073	685
chr1	110064419	110064567	E073	879
chr1	110072201	110072305	E073	8661
chr1	110072314	110072386	E073	8774
chr1	110072485	110073884	E073	8945
chr1	110073981	110074056	E073	10441
chr1	110074119	110074176	E073	10579
chr1	110074250	110074300	E073	10710
chr1	110074338	110074451	E073	10798
chr1	110074527	110074725	E073	10987
chr1	110075832	110075928	E073	12292
chr1	110078077	110078174	E073	14537
chr1	110078199	110078303	E073	14659
chr1	110078560	110079130	E073	15020
chr1	110079196	110079338	E073	15656
chr1	110084401	110084529	E073	20861
chr1	110087212	110087366	E073	23672
chr1	110105884	110105949	E073	42344
chr1	110105989	110106400	E073	42449
chr1	110106523	110106583	E073	42983
chr1	110035968	110036049	E074	-27491
chr1	110036059	110036099	E074	-27441
chr1	110036107	110036179	E074	-27361
chr1	110053049	110053213	E074	-10327
chr1	110072201	110072305	E074	8661
chr1	110072314	110072386	E074	8774
chr1	110072485	110073884	E074	8945
chr1	110073981	110074056	E074	10441
chr1	110074119	110074176	E074	10579
chr1	110074250	110074300	E074	10710
chr1	110074338	110074451	E074	10798
chr1	110078077	110078174	E074	14537
chr1	110078199	110078303	E074	14659
chr1	110078560	110079130	E074	15020
chr1	110079196	110079338	E074	15656
chr1	110098400	110098572	E074	34860
chr1	110105884	110105949	E074	42344
chr1	110105989	110106400	E074	42449
chr1	110106523	110106583	E074	42983
chr1	110106587	110106647	E074	43047
chr1	110106772	110106844	E074	43232
chr1	110106951	110107356	E074	43411
chr1	110110588	110110792	E074	47048
chr1	110111719	110111819	E074	48179
chr1	110111872	110111952	E074	48332
chr1	110112108	110112184	E074	48568
chr1	110113013	110113521	E074	49473
chr1	110028014	110028058	E081	-35482
chr1	110028135	110028380	E081	-35160
chr1	110028454	110028510	E081	-35030
chr1	110028685	110028751	E081	-34789
chr1	110028806	110028860	E081	-34680
chr1	110035747	110035946	E081	-27594
chr1	110035968	110036049	E081	-27491
chr1	110036059	110036099	E081	-27441
chr1	110036107	110036179	E081	-27361
chr1	110040305	110040378	E081	-23162
chr1	110040500	110041442	E081	-22098
chr1	110053049	110053213	E081	-10327
chr1	110053266	110053341	E081	-10199
chr1	110063987	110064120	E081	447
chr1	110064225	110064413	E081	685
chr1	110064419	110064567	E081	879
chr1	110072201	110072305	E081	8661
chr1	110072314	110072386	E081	8774
chr1	110072485	110073884	E081	8945
chr1	110073981	110074056	E081	10441
chr1	110074119	110074176	E081	10579
chr1	110074250	110074300	E081	10710
chr1	110074338	110074451	E081	10798
chr1	110074527	110074725	E081	10987
chr1	110078199	110078303	E081	14659
chr1	110078560	110079130	E081	15020
chr1	110079196	110079338	E081	15656
chr1	110098400	110098572	E081	34860
chr1	110098635	110098775	E081	35095
chr1	110098985	110099113	E081	35445
chr1	110024855	110025177	E082	-38363
chr1	110025332	110025437	E082	-38103
chr1	110028454	110028510	E082	-35030
chr1	110035968	110036049	E082	-27491
chr1	110036059	110036099	E082	-27441
chr1	110036107	110036179	E082	-27361
chr1	110040305	110040378	E082	-23162
chr1	110040500	110041442	E082	-22098
chr1	110042923	110043019	E082	-20521
chr1	110043169	110043215	E082	-20325
chr1	110043229	110043273	E082	-20267
chr1	110043289	110043329	E082	-20211
chr1	110043413	110043556	E082	-19984
chr1	110043610	110043988	E082	-19552
chr1	110072485	110073884	E082	8945
chr1	110073981	110074056	E082	10441
chr1	110078077	110078174	E082	14537
chr1	110078199	110078303	E082	14659
chr1	110078560	110079130	E082	15020
chr1	110079196	110079338	E082	15656

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	110025507	110027636	E067	-35904
chr1	110036184	110037220	E067	-26320
chr1	110037306	110037352	E067	-26188
chr1	110051714	110051851	E067	-11689
chr1	110051874	110051981	E067	-11559
chr1	110052026	110052765	E067	-10775
chr1	110089889	110092062	E067	26349
chr1	110025507	110027636	E068	-35904
chr1	110036184	110037220	E068	-26320
chr1	110037306	110037352	E068	-26188
chr1	110051714	110051851	E068	-11689
chr1	110051874	110051981	E068	-11559
chr1	110052026	110052765	E068	-10775
chr1	110089889	110092062	E068	26349
chr1	110025507	110027636	E069	-35904
chr1	110036184	110037220	E069	-26320
chr1	110037306	110037352	E069	-26188
chr1	110051714	110051851	E069	-11689
chr1	110051874	110051981	E069	-11559
chr1	110052026	110052765	E069	-10775
chr1	110089889	110092062	E069	26349
chr1	110025507	110027636	E070	-35904
chr1	110036184	110037220	E070	-26320
chr1	110037306	110037352	E070	-26188
chr1	110051714	110051851	E070	-11689
chr1	110051874	110051981	E070	-11559
chr1	110052026	110052765	E070	-10775
chr1	110089889	110092062	E070	26349
chr1	110025507	110027636	E071	-35904
chr1	110036184	110037220	E071	-26320
chr1	110037306	110037352	E071	-26188
chr1	110051714	110051851	E071	-11689
chr1	110051874	110051981	E071	-11559
chr1	110052026	110052765	E071	-10775
chr1	110089889	110092062	E071	26349
chr1	110025507	110027636	E072	-35904
chr1	110036184	110037220	E072	-26320
chr1	110037306	110037352	E072	-26188
chr1	110051714	110051851	E072	-11689
chr1	110051874	110051981	E072	-11559
chr1	110052026	110052765	E072	-10775
chr1	110089889	110092062	E072	26349
chr1	110025507	110027636	E073	-35904
chr1	110036184	110037220	E073	-26320
chr1	110037306	110037352	E073	-26188
chr1	110051714	110051851	E073	-11689
chr1	110051874	110051981	E073	-11559
chr1	110052026	110052765	E073	-10775
chr1	110089889	110092062	E073	26349
chr1	110025507	110027636	E074	-35904
chr1	110036184	110037220	E074	-26320
chr1	110037306	110037352	E074	-26188
chr1	110051714	110051851	E074	-11689
chr1	110051874	110051981	E074	-11559
chr1	110052026	110052765	E074	-10775
chr1	110089889	110092062	E074	26349
chr1	110025507	110027636	E081	-35904
chr1	110052026	110052765	E081	-10775
chr1	110089889	110092062	E081	26349
chr1	110025507	110027636	E082	-35904
chr1	110036184	110037220	E082	-26320
chr1	110037306	110037352	E082	-26188
chr1	110051714	110051851	E082	-11689
chr1	110051874	110051981	E082	-11559
chr1	110052026	110052765	E082	-10775
chr1	110089889	110092062	E082	26349