rs6677291

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0273 (8200/29942,GnomAD)
T=0274 (7995/29118,TOPMED)
T=0289 (1445/5008,1000G)
T=0244 (939/3854,ALSPAC)
T=0240 (891/3708,TWINSUK)

Position: chr1:109513504 (GRCh38.p7) (1p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 287 Enhancers around

Promoter: 79 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.109513504C>T
GRCh37.p13 chr 1	NC_000001.10:g.110056126C>T

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.638	T=0.362
1000Genomes	American	Sub	694	C=0.840	T=0.160
1000Genomes	East Asian	Sub	1008	C=0.706	T=0.294
1000Genomes	Europe	Sub	1006	C=0.770	T=0.230
1000Genomes	Global	Study-wide	5008	C=0.711	T=0.289
1000Genomes	South Asian	Sub	978	C=0.660	T=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.756	T=0.244
The Genome Aggregation Database	African	Sub	8706	C=0.671	T=0.329
The Genome Aggregation Database	American	Sub	836	C=0.830	T=0.170
The Genome Aggregation Database	East Asian	Sub	1612	C=0.725	T=0.275
The Genome Aggregation Database	Europe	Sub	18486	C=0.746	T=0.253
The Genome Aggregation Database	Global	Study-wide	29942	C=0.726	T=0.273
The Genome Aggregation Database	Other	Sub	302	C=0.760	T=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.725	T=0.274
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.760	T=0.240

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
rs6677291	9.35E-05	alcohol withdrawal symptoms	22072270

eQTL of rs6677291 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:110056126	SYPL2	ENSG00000143028.7	C>T	1.5811e-10	46946	Cerebellum

meQTL of rs6677291 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	-27746
chr1	110035747	110035946	E067	-20180
chr1	110035968	110036049	E067	-20077
chr1	110036059	110036099	E067	-20027
chr1	110036107	110036179	E067	-19947
chr1	110040305	110040378	E067	-15748
chr1	110040500	110041442	E067	-14684
chr1	110041569	110041630	E067	-14496
chr1	110041744	110041979	E067	-14147
chr1	110042000	110042040	E067	-14086
chr1	110042286	110042922	E067	-13204
chr1	110042923	110043019	E067	-13107
chr1	110043169	110043215	E067	-12911
chr1	110043229	110043273	E067	-12853
chr1	110043289	110043329	E067	-12797
chr1	110043413	110043556	E067	-12570
chr1	110043610	110043988	E067	-12138
chr1	110050718	110050768	E067	-5358
chr1	110051027	110051117	E067	-5009
chr1	110053049	110053213	E067	-2913
chr1	110053266	110053341	E067	-2785
chr1	110072201	110072305	E067	16075
chr1	110072314	110072386	E067	16188
chr1	110072485	110073884	E067	16359
chr1	110073981	110074056	E067	17855
chr1	110074119	110074176	E067	17993
chr1	110074250	110074300	E067	18124
chr1	110074338	110074451	E067	18212
chr1	110074527	110074725	E067	18401
chr1	110078077	110078174	E067	21951
chr1	110078199	110078303	E067	22073
chr1	110078560	110079130	E067	22434
chr1	110079196	110079338	E067	23070
chr1	110105884	110105949	E067	49758
chr1	110035747	110035946	E068	-20180
chr1	110035968	110036049	E068	-20077
chr1	110036059	110036099	E068	-20027
chr1	110036107	110036179	E068	-19947
chr1	110040305	110040378	E068	-15748
chr1	110040500	110041442	E068	-14684
chr1	110041569	110041630	E068	-14496
chr1	110041744	110041979	E068	-14147
chr1	110042286	110042922	E068	-13204
chr1	110042923	110043019	E068	-13107
chr1	110043169	110043215	E068	-12911
chr1	110043229	110043273	E068	-12853
chr1	110043289	110043329	E068	-12797
chr1	110043413	110043556	E068	-12570
chr1	110043610	110043988	E068	-12138
chr1	110053266	110053341	E068	-2785
chr1	110072201	110072305	E068	16075
chr1	110072314	110072386	E068	16188
chr1	110072485	110073884	E068	16359
chr1	110073981	110074056	E068	17855
chr1	110074119	110074176	E068	17993
chr1	110074250	110074300	E068	18124
chr1	110074338	110074451	E068	18212
chr1	110074527	110074725	E068	18401
chr1	110078077	110078174	E068	21951
chr1	110078199	110078303	E068	22073
chr1	110078560	110079130	E068	22434
chr1	110079196	110079338	E068	23070
chr1	110105884	110105949	E068	49758
chr1	110028454	110028510	E069	-27616
chr1	110035747	110035946	E069	-20180
chr1	110035968	110036049	E069	-20077
chr1	110036059	110036099	E069	-20027
chr1	110036107	110036179	E069	-19947
chr1	110038933	110038984	E069	-17142
chr1	110039414	110039464	E069	-16662
chr1	110040305	110040378	E069	-15748
chr1	110050718	110050768	E069	-5358
chr1	110051027	110051117	E069	-5009
chr1	110053266	110053341	E069	-2785
chr1	110072201	110072305	E069	16075
chr1	110072314	110072386	E069	16188
chr1	110072485	110073884	E069	16359
chr1	110073981	110074056	E069	17855
chr1	110074119	110074176	E069	17993
chr1	110074250	110074300	E069	18124
chr1	110074338	110074451	E069	18212
chr1	110074527	110074725	E069	18401
chr1	110078199	110078303	E069	22073
chr1	110078560	110079130	E069	22434
chr1	110079196	110079338	E069	23070
chr1	110082405	110082583	E069	26279
chr1	110105884	110105949	E069	49758
chr1	110028454	110028510	E070	-27616
chr1	110028685	110028751	E070	-27375
chr1	110028806	110028860	E070	-27266
chr1	110030010	110030131	E070	-25995
chr1	110030275	110030353	E070	-25773
chr1	110030393	110030443	E070	-25683
chr1	110030502	110030622	E070	-25504
chr1	110035747	110035946	E070	-20180
chr1	110035968	110036049	E070	-20077
chr1	110036059	110036099	E070	-20027
chr1	110036107	110036179	E070	-19947
chr1	110040305	110040378	E070	-15748
chr1	110040500	110041442	E070	-14684
chr1	110041569	110041630	E070	-14496
chr1	110041744	110041979	E070	-14147
chr1	110042000	110042040	E070	-14086
chr1	110042286	110042922	E070	-13204
chr1	110042923	110043019	E070	-13107
chr1	110043169	110043215	E070	-12911
chr1	110043229	110043273	E070	-12853
chr1	110043289	110043329	E070	-12797
chr1	110043413	110043556	E070	-12570
chr1	110043610	110043988	E070	-12138
chr1	110053266	110053341	E070	-2785
chr1	110063562	110063940	E070	7436
chr1	110064419	110064567	E070	8293
chr1	110072201	110072305	E070	16075
chr1	110072314	110072386	E070	16188
chr1	110072485	110073884	E070	16359
chr1	110073981	110074056	E070	17855
chr1	110074119	110074176	E070	17993
chr1	110074250	110074300	E070	18124
chr1	110074338	110074451	E070	18212
chr1	110074527	110074725	E070	18401
chr1	110078077	110078174	E070	21951
chr1	110078199	110078303	E070	22073
chr1	110078560	110079130	E070	22434
chr1	110033101	110033686	E071	-22440
chr1	110033689	110033979	E071	-22147
chr1	110035968	110036049	E071	-20077
chr1	110036059	110036099	E071	-20027
chr1	110036107	110036179	E071	-19947
chr1	110041569	110041630	E071	-14496
chr1	110041744	110041979	E071	-14147
chr1	110042286	110042922	E071	-13204
chr1	110042923	110043019	E071	-13107
chr1	110043169	110043215	E071	-12911
chr1	110043229	110043273	E071	-12853
chr1	110043289	110043329	E071	-12797
chr1	110043413	110043556	E071	-12570
chr1	110043610	110043988	E071	-12138
chr1	110053049	110053213	E071	-2913
chr1	110072201	110072305	E071	16075
chr1	110072314	110072386	E071	16188
chr1	110072485	110073884	E071	16359
chr1	110073981	110074056	E071	17855
chr1	110074119	110074176	E071	17993
chr1	110074250	110074300	E071	18124
chr1	110074338	110074451	E071	18212
chr1	110074527	110074725	E071	18401
chr1	110078077	110078174	E071	21951
chr1	110078199	110078303	E071	22073
chr1	110078560	110079130	E071	22434
chr1	110079196	110079338	E071	23070
chr1	110082405	110082583	E071	26279
chr1	110105884	110105949	E071	49758
chr1	110028014	110028058	E072	-28068
chr1	110028135	110028380	E072	-27746
chr1	110033101	110033686	E072	-22440
chr1	110035968	110036049	E072	-20077
chr1	110036059	110036099	E072	-20027
chr1	110036107	110036179	E072	-19947
chr1	110038933	110038984	E072	-17142
chr1	110040305	110040378	E072	-15748
chr1	110040500	110041442	E072	-14684
chr1	110041569	110041630	E072	-14496
chr1	110041744	110041979	E072	-14147
chr1	110042000	110042040	E072	-14086
chr1	110042286	110042922	E072	-13204
chr1	110042923	110043019	E072	-13107
chr1	110043169	110043215	E072	-12911
chr1	110043229	110043273	E072	-12853
chr1	110043289	110043329	E072	-12797
chr1	110043413	110043556	E072	-12570
chr1	110043610	110043988	E072	-12138
chr1	110050718	110050768	E072	-5358
chr1	110051027	110051117	E072	-5009
chr1	110070849	110070919	E072	14723
chr1	110072201	110072305	E072	16075
chr1	110072314	110072386	E072	16188
chr1	110072485	110073884	E072	16359
chr1	110073981	110074056	E072	17855
chr1	110074119	110074176	E072	17993
chr1	110074250	110074300	E072	18124
chr1	110074338	110074451	E072	18212
chr1	110078199	110078303	E072	22073
chr1	110078560	110079130	E072	22434
chr1	110105884	110105949	E072	49758
chr1	110028014	110028058	E073	-28068
chr1	110028135	110028380	E073	-27746
chr1	110033101	110033686	E073	-22440
chr1	110033689	110033979	E073	-22147
chr1	110035603	110035704	E073	-20422
chr1	110040305	110040378	E073	-15748
chr1	110040500	110041442	E073	-14684
chr1	110041569	110041630	E073	-14496
chr1	110041744	110041979	E073	-14147
chr1	110042000	110042040	E073	-14086
chr1	110042286	110042922	E073	-13204
chr1	110042923	110043019	E073	-13107
chr1	110043169	110043215	E073	-12911
chr1	110043229	110043273	E073	-12853
chr1	110043289	110043329	E073	-12797
chr1	110043413	110043556	E073	-12570
chr1	110043610	110043988	E073	-12138
chr1	110064225	110064413	E073	8099
chr1	110064419	110064567	E073	8293
chr1	110072201	110072305	E073	16075
chr1	110072314	110072386	E073	16188
chr1	110072485	110073884	E073	16359
chr1	110073981	110074056	E073	17855
chr1	110074119	110074176	E073	17993
chr1	110074250	110074300	E073	18124
chr1	110074338	110074451	E073	18212
chr1	110074527	110074725	E073	18401
chr1	110075832	110075928	E073	19706
chr1	110078077	110078174	E073	21951
chr1	110078199	110078303	E073	22073
chr1	110078560	110079130	E073	22434
chr1	110079196	110079338	E073	23070
chr1	110084401	110084529	E073	28275
chr1	110087212	110087366	E073	31086
chr1	110105884	110105949	E073	49758
chr1	110035968	110036049	E074	-20077
chr1	110036059	110036099	E074	-20027
chr1	110036107	110036179	E074	-19947
chr1	110053049	110053213	E074	-2913
chr1	110072201	110072305	E074	16075
chr1	110072314	110072386	E074	16188
chr1	110072485	110073884	E074	16359
chr1	110073981	110074056	E074	17855
chr1	110074119	110074176	E074	17993
chr1	110074250	110074300	E074	18124
chr1	110074338	110074451	E074	18212
chr1	110078077	110078174	E074	21951
chr1	110078199	110078303	E074	22073
chr1	110078560	110079130	E074	22434
chr1	110079196	110079338	E074	23070
chr1	110098400	110098572	E074	42274
chr1	110105884	110105949	E074	49758
chr1	110028014	110028058	E081	-28068
chr1	110028135	110028380	E081	-27746
chr1	110028454	110028510	E081	-27616
chr1	110028685	110028751	E081	-27375
chr1	110028806	110028860	E081	-27266
chr1	110035747	110035946	E081	-20180
chr1	110035968	110036049	E081	-20077
chr1	110036059	110036099	E081	-20027
chr1	110036107	110036179	E081	-19947
chr1	110040305	110040378	E081	-15748
chr1	110040500	110041442	E081	-14684
chr1	110053049	110053213	E081	-2913
chr1	110053266	110053341	E081	-2785
chr1	110063987	110064120	E081	7861
chr1	110064225	110064413	E081	8099
chr1	110064419	110064567	E081	8293
chr1	110072201	110072305	E081	16075
chr1	110072314	110072386	E081	16188
chr1	110072485	110073884	E081	16359
chr1	110073981	110074056	E081	17855
chr1	110074119	110074176	E081	17993
chr1	110074250	110074300	E081	18124
chr1	110074338	110074451	E081	18212
chr1	110074527	110074725	E081	18401
chr1	110078199	110078303	E081	22073
chr1	110078560	110079130	E081	22434
chr1	110079196	110079338	E081	23070
chr1	110098400	110098572	E081	42274
chr1	110098635	110098775	E081	42509
chr1	110098985	110099113	E081	42859
chr1	110024855	110025177	E082	-30949
chr1	110025332	110025437	E082	-30689
chr1	110028454	110028510	E082	-27616
chr1	110035968	110036049	E082	-20077
chr1	110036059	110036099	E082	-20027
chr1	110036107	110036179	E082	-19947
chr1	110040305	110040378	E082	-15748
chr1	110040500	110041442	E082	-14684
chr1	110042923	110043019	E082	-13107
chr1	110043169	110043215	E082	-12911
chr1	110043229	110043273	E082	-12853
chr1	110043289	110043329	E082	-12797
chr1	110043413	110043556	E082	-12570
chr1	110043610	110043988	E082	-12138
chr1	110072485	110073884	E082	16359
chr1	110073981	110074056	E082	17855
chr1	110078077	110078174	E082	21951
chr1	110078199	110078303	E082	22073
chr1	110078560	110079130	E082	22434
chr1	110079196	110079338	E082	23070

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	110008742	110008796	E067	-47330
chr1	110008818	110009858	E067	-46268
chr1	110009911	110010302	E067	-45824
chr1	110025507	110027636	E067	-28490
chr1	110036184	110037220	E067	-18906
chr1	110037306	110037352	E067	-18774
chr1	110051714	110051851	E067	-4275
chr1	110051874	110051981	E067	-4145
chr1	110052026	110052765	E067	-3361
chr1	110089889	110092062	E067	33763
chr1	110008818	110009858	E068	-46268
chr1	110025507	110027636	E068	-28490
chr1	110036184	110037220	E068	-18906
chr1	110037306	110037352	E068	-18774
chr1	110051714	110051851	E068	-4275
chr1	110051874	110051981	E068	-4145
chr1	110052026	110052765	E068	-3361
chr1	110089889	110092062	E068	33763
chr1	110008818	110009858	E069	-46268
chr1	110025507	110027636	E069	-28490
chr1	110036184	110037220	E069	-18906
chr1	110037306	110037352	E069	-18774
chr1	110051714	110051851	E069	-4275
chr1	110051874	110051981	E069	-4145
chr1	110052026	110052765	E069	-3361
chr1	110089889	110092062	E069	33763
chr1	110025507	110027636	E070	-28490
chr1	110036184	110037220	E070	-18906
chr1	110037306	110037352	E070	-18774
chr1	110051714	110051851	E070	-4275
chr1	110051874	110051981	E070	-4145
chr1	110052026	110052765	E070	-3361
chr1	110089889	110092062	E070	33763
chr1	110008742	110008796	E071	-47330
chr1	110008818	110009858	E071	-46268
chr1	110009911	110010302	E071	-45824
chr1	110025507	110027636	E071	-28490
chr1	110036184	110037220	E071	-18906
chr1	110037306	110037352	E071	-18774
chr1	110051714	110051851	E071	-4275
chr1	110051874	110051981	E071	-4145
chr1	110052026	110052765	E071	-3361
chr1	110089889	110092062	E071	33763
chr1	110008818	110009858	E072	-46268
chr1	110025507	110027636	E072	-28490
chr1	110036184	110037220	E072	-18906
chr1	110037306	110037352	E072	-18774
chr1	110051714	110051851	E072	-4275
chr1	110051874	110051981	E072	-4145
chr1	110052026	110052765	E072	-3361
chr1	110089889	110092062	E072	33763
chr1	110008818	110009858	E073	-46268
chr1	110025507	110027636	E073	-28490
chr1	110036184	110037220	E073	-18906
chr1	110037306	110037352	E073	-18774
chr1	110051714	110051851	E073	-4275
chr1	110051874	110051981	E073	-4145
chr1	110052026	110052765	E073	-3361
chr1	110089889	110092062	E073	33763
chr1	110008742	110008796	E074	-47330
chr1	110008818	110009858	E074	-46268
chr1	110025507	110027636	E074	-28490
chr1	110036184	110037220	E074	-18906
chr1	110037306	110037352	E074	-18774
chr1	110051714	110051851	E074	-4275
chr1	110051874	110051981	E074	-4145
chr1	110052026	110052765	E074	-3361
chr1	110089889	110092062	E074	33763
chr1	110025507	110027636	E081	-28490
chr1	110052026	110052765	E081	-3361
chr1	110089889	110092062	E081	33763
chr1	110008818	110009858	E082	-46268
chr1	110025507	110027636	E082	-28490
chr1	110036184	110037220	E082	-18906
chr1	110037306	110037352	E082	-18774
chr1	110051714	110051851	E082	-4275
chr1	110051874	110051981	E082	-4145
chr1	110052026	110052765	E082	-3361
chr1	110089889	110092062	E082	33763