rs12241232

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SLF2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0264 (7741/29320,GnomAD)
C=0285 (8301/29118,TOPMED)
C=0361 (1807/5008,1000G)
C=0203 (783/3854,ALSPAC)
C=0210 (777/3708,TWINSUK)

Position: chr10:100932847 (GRCh38.p7) (10q24.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 3 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.100932847T>C
GRCh37.p13 chr 10	NC_000010.10:g.102692604T>C

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

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.616	C=0.384
1000Genomes	American	Sub	694	T=0.720	C=0.280
1000Genomes	East Asian	Sub	1008	T=0.454	C=0.546
1000Genomes	Europe	Sub	1006	T=0.818	C=0.182
1000Genomes	Global	Study-wide	5008	T=0.639	C=0.361
1000Genomes	South Asian	Sub	978	T=0.620	C=0.380
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.797	C=0.203
The Genome Aggregation Database	African	Sub	8656	T=0.658	C=0.342
The Genome Aggregation Database	American	Sub	828	T=0.660	C=0.340
The Genome Aggregation Database	East Asian	Sub	1606	T=0.422	C=0.578
The Genome Aggregation Database	Europe	Sub	17930	T=0.803	C=0.196
The Genome Aggregation Database	Global	Study-wide	29320	T=0.736	C=0.264
The Genome Aggregation Database	Other	Sub	300	T=0.830	C=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.714	C=0.285
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.790	C=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
19128478	Complex nature of SNP genotype effects on gene expression in primary human leucocytes.	Heap GA	BMC Med Genomics
19680542	Tissue effect on genetic control of transcript isoform variation.	Kwan T	PLoS Genet

SNP ID	p-value	Traits	Study
rs12241232	0.000489	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr10:102692604	MRPL43	ENSG00000055950.12	T>C	2.1437e-6	-54519	Cerebellum
Chr10:102692604	MRPL43	ENSG00000055950.12	T>C	5.5041e-5	-54519	Hypothalamus
Chr10:102692604	MRPL43	ENSG00000055950.12	T>C	3.6980e-5	-54519	Cerebellar_Hemisphere
Chr10:102692604	MRPL43	ENSG00000055950.12	T>C	8.3858e-4	-54519	Caudate_basal_ganglia

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	-18071
chr10	102674541	102674593	E067	-18011
chr10	102674968	102675018	E067	-17586
chr10	102675403	102675463	E067	-17141
chr10	102676362	102676412	E067	-16192
chr10	102676481	102676628	E067	-15976
chr10	102676638	102676692	E067	-15912
chr10	102676756	102676806	E067	-15798
chr10	102676818	102676872	E067	-15732
chr10	102676899	102676949	E067	-15655
chr10	102677375	102677419	E067	-15185
chr10	102690202	102690318	E067	-2286
chr10	102690474	102690564	E067	-2040
chr10	102691014	102691071	E067	-1533
chr10	102728355	102728532	E067	35751
chr10	102646354	102647408	E068	-45196
chr10	102670160	102670220	E068	-22384
chr10	102674968	102675018	E068	-17586
chr10	102675403	102675463	E068	-17141
chr10	102676481	102676628	E068	-15976
chr10	102676638	102676692	E068	-15912
chr10	102676756	102676806	E068	-15798
chr10	102683095	102683208	E068	-9396
chr10	102683392	102683573	E068	-9031
chr10	102690123	102690173	E068	-2431
chr10	102690202	102690318	E068	-2286
chr10	102690474	102690564	E068	-2040
chr10	102728355	102728532	E068	35751
chr10	102669163	102670039	E069	-22565
chr10	102676756	102676806	E069	-15798
chr10	102676818	102676872	E069	-15732
chr10	102676899	102676949	E069	-15655
chr10	102677375	102677419	E069	-15185
chr10	102683095	102683208	E069	-9396
chr10	102683392	102683573	E069	-9031
chr10	102690202	102690318	E069	-2286
chr10	102690474	102690564	E069	-2040
chr10	102691014	102691071	E069	-1533
chr10	102691674	102691724	E069	-880
chr10	102691877	102691955	E069	-649
chr10	102727954	102728353	E069	35350
chr10	102728355	102728532	E069	35751
chr10	102671405	102671458	E070	-21146
chr10	102674427	102674533	E070	-18071
chr10	102674541	102674593	E070	-18011
chr10	102649430	102649490	E071	-43114
chr10	102669163	102670039	E071	-22565
chr10	102674427	102674533	E071	-18071
chr10	102674541	102674593	E071	-18011
chr10	102674968	102675018	E071	-17586
chr10	102675403	102675463	E071	-17141
chr10	102676481	102676628	E071	-15976
chr10	102676638	102676692	E071	-15912
chr10	102676756	102676806	E071	-15798
chr10	102676818	102676872	E071	-15732
chr10	102676899	102676949	E071	-15655
chr10	102683095	102683208	E071	-9396
chr10	102683392	102683573	E071	-9031
chr10	102690123	102690173	E071	-2431
chr10	102690202	102690318	E071	-2286
chr10	102690474	102690564	E071	-2040
chr10	102691014	102691071	E071	-1533
chr10	102691674	102691724	E071	-880
chr10	102691877	102691955	E071	-649
chr10	102692474	102692524	E071	-80
chr10	102727954	102728353	E071	35350
chr10	102728355	102728532	E071	35751
chr10	102675403	102675463	E072	-17141
chr10	102683095	102683208	E072	-9396
chr10	102683392	102683573	E072	-9031
chr10	102690123	102690173	E072	-2431
chr10	102690202	102690318	E072	-2286
chr10	102690474	102690564	E072	-2040
chr10	102691674	102691724	E072	-880
chr10	102691877	102691955	E072	-649
chr10	102692474	102692524	E072	-80
chr10	102728355	102728532	E072	35751
chr10	102674968	102675018	E073	-17586
chr10	102728355	102728532	E073	35751
chr10	102669163	102670039	E074	-22565
chr10	102670160	102670220	E074	-22384
chr10	102674427	102674533	E074	-18071
chr10	102674541	102674593	E074	-18011
chr10	102674968	102675018	E074	-17586
chr10	102675403	102675463	E074	-17141
chr10	102676362	102676412	E074	-16192
chr10	102676481	102676628	E074	-15976
chr10	102676638	102676692	E074	-15912
chr10	102676756	102676806	E074	-15798
chr10	102676818	102676872	E074	-15732
chr10	102676899	102676949	E074	-15655
chr10	102683095	102683208	E074	-9396
chr10	102683392	102683573	E074	-9031
chr10	102690123	102690173	E074	-2431
chr10	102690202	102690318	E074	-2286
chr10	102690474	102690564	E074	-2040
chr10	102691014	102691071	E074	-1533
chr10	102691674	102691724	E074	-880
chr10	102691877	102691955	E074	-649
chr10	102692474	102692524	E074	-80
chr10	102728355	102728532	E074	35751
chr10	102670374	102670434	E081	-22170
chr10	102670442	102670575	E081	-22029
chr10	102670652	102670749	E081	-21855
chr10	102670828	102670878	E081	-21726
chr10	102670906	102670971	E081	-21633
chr10	102671126	102671176	E081	-21428
chr10	102671203	102671363	E081	-21241
chr10	102671405	102671458	E081	-21146
chr10	102674427	102674533	E081	-18071
chr10	102674541	102674593	E081	-18011
chr10	102727791	102727838	E081	35187
chr10	102727954	102728353	E081	35350
chr10	102728355	102728532	E081	35751
chr10	102727791	102727838	E082	35187

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr10	102671564	102673803	E067	-18801
chr10	102671564	102673803	E068	-18801
chr10	102671564	102673803	E069	-18801
chr10	102671564	102673803	E070	-18801
chr10	102671564	102673803	E071	-18801
chr10	102671564	102673803	E072	-18801
chr10	102671564	102673803	E073	-18801
chr10	102728545	102731770	E073	35941
chr10	102671564	102673803	E074	-18801
chr10	102671564	102673803	E081	-18801
chr10	102671564	102673803	E082	-18801
chr10	102728545	102731770	E082	35941

rs12241232

Genomic Coordinates

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

Population Frequency

P-Value

eQTL of rs12241232 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs12241232 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)