rs7911957

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SLF2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0259 (7753/29936,GnomAD)
G=0285 (8303/29118,TOPMED)
G=0361 (1808/5008,1000G)
G=0203 (782/3854,ALSPAC)
G=0210 (777/3708,TWINSUK)

Position: chr10:100933213 (GRCh38.p7) (10q24.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 115 Enhancers around

Promoter: 12 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 10	NC_000010.11:g.100933213A>G
GRCh37.p13 chr 10	NC_000010.10:g.102692970A>G

Gene: SLF2, SMC5-SMC6 complex localization factor 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLF2 transcript variant 2	NM_001136123.1:c.	N/A	Intron Variant
SLF2 transcript variant 1	NM_018121.3:c.	N/A	Intron Variant
SLF2 transcript variant 3	NM_001243770.1:c.	N/A	Genic Downstream Transcript Variant
SLF2 transcript variant X1	XM_005269965.2:c.	N/A	Intron Variant
SLF2 transcript variant X2	XM_011539944.2:c.	N/A	Intron Variant
SLF2 transcript variant X3	XR_001747138.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.616	G=0.384
1000Genomes	American	Sub	694	A=0.720	G=0.280
1000Genomes	East Asian	Sub	1008	A=0.454	G=0.546
1000Genomes	Europe	Sub	1006	A=0.818	G=0.182
1000Genomes	Global	Study-wide	5008	A=0.639	G=0.361
1000Genomes	South Asian	Sub	978	A=0.620	G=0.380
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.797	G=0.203
The Genome Aggregation Database	African	Sub	8708	A=0.660	G=0.340
The Genome Aggregation Database	American	Sub	838	A=0.670	G=0.330
The Genome Aggregation Database	East Asian	Sub	1614	A=0.424	G=0.576
The Genome Aggregation Database	Europe	Sub	18474	A=0.808	G=0.191
The Genome Aggregation Database	Global	Study-wide	29936	A=0.741	G=0.259
The Genome Aggregation Database	Other	Sub	302	A=0.830	G=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.714	G=0.285
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.790	G=0.210

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
rs7911957	0.000337	alcohol dependence	20201924

eQTL of rs7911957 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr10:102692970	MRPL43	ENSG00000055950.12	A>G	2.1437e-6	-54153	Cerebellum
Chr10:102692970	MRPL43	ENSG00000055950.12	A>G	5.5041e-5	-54153	Hypothalamus
Chr10:102692970	MRPL43	ENSG00000055950.12	A>G	3.6980e-5	-54153	Cerebellar_Hemisphere
Chr10:102692970	MRPL43	ENSG00000055950.12	A>G	8.3858e-4	-54153	Caudate_basal_ganglia

meQTL of rs7911957 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 )
chr10	102674427	102674533	E067	-18437
chr10	102674541	102674593	E067	-18377
chr10	102674968	102675018	E067	-17952
chr10	102675403	102675463	E067	-17507
chr10	102676362	102676412	E067	-16558
chr10	102676481	102676628	E067	-16342
chr10	102676638	102676692	E067	-16278
chr10	102676756	102676806	E067	-16164
chr10	102676818	102676872	E067	-16098
chr10	102676899	102676949	E067	-16021
chr10	102677375	102677419	E067	-15551
chr10	102690202	102690318	E067	-2652
chr10	102690474	102690564	E067	-2406
chr10	102691014	102691071	E067	-1899
chr10	102728355	102728532	E067	35385
chr10	102646354	102647408	E068	-45562
chr10	102670160	102670220	E068	-22750
chr10	102674968	102675018	E068	-17952
chr10	102675403	102675463	E068	-17507
chr10	102676481	102676628	E068	-16342
chr10	102676638	102676692	E068	-16278
chr10	102676756	102676806	E068	-16164
chr10	102683095	102683208	E068	-9762
chr10	102683392	102683573	E068	-9397
chr10	102690123	102690173	E068	-2797
chr10	102690202	102690318	E068	-2652
chr10	102690474	102690564	E068	-2406
chr10	102728355	102728532	E068	35385
chr10	102669163	102670039	E069	-22931
chr10	102676756	102676806	E069	-16164
chr10	102676818	102676872	E069	-16098
chr10	102676899	102676949	E069	-16021
chr10	102677375	102677419	E069	-15551
chr10	102683095	102683208	E069	-9762
chr10	102683392	102683573	E069	-9397
chr10	102690202	102690318	E069	-2652
chr10	102690474	102690564	E069	-2406
chr10	102691014	102691071	E069	-1899
chr10	102691674	102691724	E069	-1246
chr10	102691877	102691955	E069	-1015
chr10	102727954	102728353	E069	34984
chr10	102728355	102728532	E069	35385
chr10	102671405	102671458	E070	-21512
chr10	102674427	102674533	E070	-18437
chr10	102674541	102674593	E070	-18377
chr10	102649430	102649490	E071	-43480
chr10	102669163	102670039	E071	-22931
chr10	102674427	102674533	E071	-18437
chr10	102674541	102674593	E071	-18377
chr10	102674968	102675018	E071	-17952
chr10	102675403	102675463	E071	-17507
chr10	102676481	102676628	E071	-16342
chr10	102676638	102676692	E071	-16278
chr10	102676756	102676806	E071	-16164
chr10	102676818	102676872	E071	-16098
chr10	102676899	102676949	E071	-16021
chr10	102683095	102683208	E071	-9762
chr10	102683392	102683573	E071	-9397
chr10	102690123	102690173	E071	-2797
chr10	102690202	102690318	E071	-2652
chr10	102690474	102690564	E071	-2406
chr10	102691014	102691071	E071	-1899
chr10	102691674	102691724	E071	-1246
chr10	102691877	102691955	E071	-1015
chr10	102692474	102692524	E071	-446
chr10	102727954	102728353	E071	34984
chr10	102728355	102728532	E071	35385
chr10	102675403	102675463	E072	-17507
chr10	102683095	102683208	E072	-9762
chr10	102683392	102683573	E072	-9397
chr10	102690123	102690173	E072	-2797
chr10	102690202	102690318	E072	-2652
chr10	102690474	102690564	E072	-2406
chr10	102691674	102691724	E072	-1246
chr10	102691877	102691955	E072	-1015
chr10	102692474	102692524	E072	-446
chr10	102728355	102728532	E072	35385
chr10	102674968	102675018	E073	-17952
chr10	102728355	102728532	E073	35385
chr10	102669163	102670039	E074	-22931
chr10	102670160	102670220	E074	-22750
chr10	102674427	102674533	E074	-18437
chr10	102674541	102674593	E074	-18377
chr10	102674968	102675018	E074	-17952
chr10	102675403	102675463	E074	-17507
chr10	102676362	102676412	E074	-16558
chr10	102676481	102676628	E074	-16342
chr10	102676638	102676692	E074	-16278
chr10	102676756	102676806	E074	-16164
chr10	102676818	102676872	E074	-16098
chr10	102676899	102676949	E074	-16021
chr10	102683095	102683208	E074	-9762
chr10	102683392	102683573	E074	-9397
chr10	102690123	102690173	E074	-2797
chr10	102690202	102690318	E074	-2652
chr10	102690474	102690564	E074	-2406
chr10	102691014	102691071	E074	-1899
chr10	102691674	102691724	E074	-1246
chr10	102691877	102691955	E074	-1015
chr10	102692474	102692524	E074	-446
chr10	102728355	102728532	E074	35385
chr10	102670374	102670434	E081	-22536
chr10	102670442	102670575	E081	-22395
chr10	102670652	102670749	E081	-22221
chr10	102670828	102670878	E081	-22092
chr10	102670906	102670971	E081	-21999
chr10	102671126	102671176	E081	-21794
chr10	102671203	102671363	E081	-21607
chr10	102671405	102671458	E081	-21512
chr10	102674427	102674533	E081	-18437
chr10	102674541	102674593	E081	-18377
chr10	102727791	102727838	E081	34821
chr10	102727954	102728353	E081	34984
chr10	102728355	102728532	E081	35385
chr10	102727791	102727838	E082	34821

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr10	102671564	102673803	E067	-19167
chr10	102671564	102673803	E068	-19167
chr10	102671564	102673803	E069	-19167
chr10	102671564	102673803	E070	-19167
chr10	102671564	102673803	E071	-19167
chr10	102671564	102673803	E072	-19167
chr10	102671564	102673803	E073	-19167
chr10	102728545	102731770	E073	35575
chr10	102671564	102673803	E074	-19167
chr10	102671564	102673803	E081	-19167
chr10	102671564	102673803	E082	-19167
chr10	102728545	102731770	E082	35575