rs10501226

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

LRRC4C : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0038 (1151/29984,GnomAD)
C=0038 (1119/29118,TOPMED)
C=0053 (266/5008,1000G)
C=0040 (154/3854,ALSPAC)
C=0031 (115/3708,TWINSUK)

Position: chr11:40280456 (GRCh38.p7) (11p12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 203 Enhancers around

Promoter: 142 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.40280456T>C
GRCh37.p13 chr 11	NC_000011.9:g.40302006T>C

Gene: LRRC4C, leucine rich repeat containing 4C(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LRRC4C transcript variant 2	NM_001258419.1:c.	N/A	Intron Variant
LRRC4C transcript variant 1	NM_020929.2:c.	N/A	Intron Variant
LRRC4C transcript variant 3	NR_047673.1:n.	N/A	Intron Variant
LRRC4C transcript variant 4	NR_047674.1:n.	N/A	Intron Variant
LRRC4C transcript variant X1	XM_011520238.2:c.	N/A	Intron Variant
LRRC4C transcript variant X2	XM_011520239.2:c.	N/A	Intron Variant
LRRC4C transcript variant X3	XM_011520240.2:c.	N/A	Intron Variant
LRRC4C transcript variant X9	XM_011520241.2:c.	N/A	Intron Variant
LRRC4C transcript variant X11	XM_011520242.2:c.	N/A	Intron Variant
LRRC4C transcript variant X8	XM_011520243.2:c.	N/A	Intron Variant
LRRC4C transcript variant X10	XM_011520244.2:c.	N/A	Intron Variant
LRRC4C transcript variant X4	XM_017018070.1:c.	N/A	Intron Variant
LRRC4C transcript variant X5	XM_017018071.1:c.	N/A	Intron Variant
LRRC4C transcript variant X6	XM_017018072.1:c.	N/A	Intron Variant
LRRC4C transcript variant X7	XM_017018073.1:c.	N/A	Intron Variant
LRRC4C transcript variant X12	XM_017018074.1:c.	N/A	Intron Variant
LRRC4C transcript variant X13	XM_017018075.1:c.	N/A	Intron Variant
LRRC4C transcript variant X14	XM_017018076.1:c.	N/A	Intron Variant
LRRC4C transcript variant X15	XM_017018077.1:c.	N/A	Intron Variant
LRRC4C transcript variant X16	XM_017018078.1:c.	N/A	Intron Variant
LRRC4C transcript variant X17	XM_017018079.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.943	C=0.057
1000Genomes	American	Sub	694	T=0.960	C=0.040
1000Genomes	East Asian	Sub	1008	T=0.980	C=0.020
1000Genomes	Europe	Sub	1006	T=0.969	C=0.031
1000Genomes	Global	Study-wide	5008	T=0.947	C=0.053
1000Genomes	South Asian	Sub	978	T=0.890	C=0.110
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.960	C=0.040
The Genome Aggregation Database	African	Sub	8732	T=0.953	C=0.047
The Genome Aggregation Database	American	Sub	838	T=0.960	C=0.040
The Genome Aggregation Database	East Asian	Sub	1614	T=0.986	C=0.014
The Genome Aggregation Database	Europe	Sub	18498	T=0.963	C=0.036
The Genome Aggregation Database	Global	Study-wide	29984	T=0.961	C=0.038
The Genome Aggregation Database	Other	Sub	302	T=0.980	C=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.961	C=0.038
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.969	C=0.031

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs10501226	0.000686	alcohol dependence	21314694

eQTL of rs10501226 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 rs10501226 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 )
chr11	40252539	40252677	E067	-49329
chr11	40273173	40273223	E067	-28783
chr11	40275773	40275827	E067	-26179
chr11	40276773	40276823	E067	-25183
chr11	40277143	40277274	E067	-24732
chr11	40290060	40290786	E067	-11220
chr11	40291578	40291723	E067	-10283
chr11	40291804	40291877	E067	-10129
chr11	40292192	40292351	E067	-9655
chr11	40292528	40292578	E067	-9428
chr11	40293083	40293137	E067	-8869
chr11	40293307	40293459	E067	-8547
chr11	40294736	40294935	E067	-7071
chr11	40295052	40295251	E067	-6755
chr11	40295348	40295613	E067	-6393
chr11	40295687	40295863	E067	-6143
chr11	40295970	40296111	E067	-5895
chr11	40296203	40296264	E067	-5742
chr11	40296720	40296774	E067	-5232
chr11	40297086	40297150	E067	-4856
chr11	40297707	40297757	E067	-4249
chr11	40298313	40298384	E067	-3622
chr11	40301296	40301373	E067	-633
chr11	40303226	40303303	E067	1220
chr11	40303507	40303603	E067	1501
chr11	40306522	40306572	E067	4516
chr11	40306890	40306997	E067	4884
chr11	40307229	40307450	E067	5223
chr11	40307613	40307663	E067	5607
chr11	40307830	40307944	E067	5824
chr11	40307959	40308142	E067	5953
chr11	40350572	40351240	E067	48566
chr11	40252539	40252677	E068	-49329
chr11	40257962	40258039	E068	-43967
chr11	40273173	40273223	E068	-28783
chr11	40273690	40273740	E068	-28266
chr11	40290060	40290786	E068	-11220
chr11	40291578	40291723	E068	-10283
chr11	40291804	40291877	E068	-10129
chr11	40292192	40292351	E068	-9655
chr11	40292528	40292578	E068	-9428
chr11	40293083	40293137	E068	-8869
chr11	40293307	40293459	E068	-8547
chr11	40295052	40295251	E068	-6755
chr11	40295348	40295613	E068	-6393
chr11	40295687	40295863	E068	-6143
chr11	40295970	40296111	E068	-5895
chr11	40296203	40296264	E068	-5742
chr11	40296720	40296774	E068	-5232
chr11	40297086	40297150	E068	-4856
chr11	40298313	40298384	E068	-3622
chr11	40298543	40298593	E068	-3413
chr11	40301296	40301373	E068	-633
chr11	40303226	40303303	E068	1220
chr11	40303507	40303603	E068	1501
chr11	40306890	40306997	E068	4884
chr11	40307229	40307450	E068	5223
chr11	40308572	40308625	E068	6566
chr11	40252539	40252677	E069	-49329
chr11	40263052	40263724	E069	-38282
chr11	40274852	40275007	E069	-26999
chr11	40275773	40275827	E069	-26179
chr11	40276773	40276823	E069	-25183
chr11	40277143	40277274	E069	-24732
chr11	40277965	40278046	E069	-23960
chr11	40291038	40291078	E069	-10928
chr11	40291578	40291723	E069	-10283
chr11	40291804	40291877	E069	-10129
chr11	40292192	40292351	E069	-9655
chr11	40292528	40292578	E069	-9428
chr11	40293083	40293137	E069	-8869
chr11	40293307	40293459	E069	-8547
chr11	40295052	40295251	E069	-6755
chr11	40295348	40295613	E069	-6393
chr11	40295687	40295863	E069	-6143
chr11	40295970	40296111	E069	-5895
chr11	40296203	40296264	E069	-5742
chr11	40297707	40297757	E069	-4249
chr11	40298313	40298384	E069	-3622
chr11	40298543	40298593	E069	-3413
chr11	40299800	40299850	E069	-2156
chr11	40300136	40300186	E069	-1820
chr11	40301296	40301373	E069	-633
chr11	40301509	40301698	E069	-308
chr11	40306522	40306572	E069	4516
chr11	40306890	40306997	E069	4884
chr11	40307229	40307450	E069	5223
chr11	40303226	40303303	E070	1220
chr11	40252539	40252677	E071	-49329
chr11	40275773	40275827	E071	-26179
chr11	40278534	40278588	E071	-23418
chr11	40286467	40286672	E071	-15334
chr11	40286811	40286918	E071	-15088
chr11	40290060	40290786	E071	-11220
chr11	40291578	40291723	E071	-10283
chr11	40291804	40291877	E071	-10129
chr11	40292192	40292351	E071	-9655
chr11	40292528	40292578	E071	-9428
chr11	40293083	40293137	E071	-8869
chr11	40293307	40293459	E071	-8547
chr11	40294736	40294935	E071	-7071
chr11	40295052	40295251	E071	-6755
chr11	40295348	40295613	E071	-6393
chr11	40295687	40295863	E071	-6143
chr11	40295970	40296111	E071	-5895
chr11	40296203	40296264	E071	-5742
chr11	40297707	40297757	E071	-4249
chr11	40298313	40298384	E071	-3622
chr11	40298543	40298593	E071	-3413
chr11	40299800	40299850	E071	-2156
chr11	40300136	40300186	E071	-1820
chr11	40301296	40301373	E071	-633
chr11	40301509	40301698	E071	-308
chr11	40303226	40303303	E071	1220
chr11	40303507	40303603	E071	1501
chr11	40306522	40306572	E071	4516
chr11	40306890	40306997	E071	4884
chr11	40307229	40307450	E071	5223
chr11	40307613	40307663	E071	5607
chr11	40307830	40307944	E071	5824
chr11	40307959	40308142	E071	5953
chr11	40308175	40308235	E071	6169
chr11	40308237	40308287	E071	6231
chr11	40308333	40308383	E071	6327
chr11	40308572	40308625	E071	6566
chr11	40350572	40351240	E071	48566
chr11	40252539	40252677	E072	-49329
chr11	40273173	40273223	E072	-28783
chr11	40273690	40273740	E072	-28266
chr11	40273929	40274015	E072	-27991
chr11	40290060	40290786	E072	-11220
chr11	40291804	40291877	E072	-10129
chr11	40292192	40292351	E072	-9655
chr11	40292528	40292578	E072	-9428
chr11	40293083	40293137	E072	-8869
chr11	40293307	40293459	E072	-8547
chr11	40295052	40295251	E072	-6755
chr11	40295348	40295613	E072	-6393
chr11	40295687	40295863	E072	-6143
chr11	40295970	40296111	E072	-5895
chr11	40296203	40296264	E072	-5742
chr11	40298313	40298384	E072	-3622
chr11	40298543	40298593	E072	-3413
chr11	40298631	40298847	E072	-3159
chr11	40301296	40301373	E072	-633
chr11	40301509	40301698	E072	-308
chr11	40308572	40308625	E072	6566
chr11	40285171	40285227	E073	-16779
chr11	40285244	40285335	E073	-16671
chr11	40295348	40295613	E073	-6393
chr11	40295687	40295863	E073	-6143
chr11	40295970	40296111	E073	-5895
chr11	40296203	40296264	E073	-5742
chr11	40297707	40297757	E073	-4249
chr11	40301296	40301373	E073	-633
chr11	40301509	40301698	E073	-308
chr11	40306522	40306572	E073	4516
chr11	40306890	40306997	E073	4884
chr11	40257470	40257625	E074	-44381
chr11	40257962	40258039	E074	-43967
chr11	40263052	40263724	E074	-38282
chr11	40275773	40275827	E074	-26179
chr11	40276773	40276823	E074	-25183
chr11	40277143	40277274	E074	-24732
chr11	40290060	40290786	E074	-11220
chr11	40292528	40292578	E074	-9428
chr11	40293083	40293137	E074	-8869
chr11	40293307	40293459	E074	-8547
chr11	40295052	40295251	E074	-6755
chr11	40295348	40295613	E074	-6393
chr11	40295687	40295863	E074	-6143
chr11	40295970	40296111	E074	-5895
chr11	40296203	40296264	E074	-5742
chr11	40296720	40296774	E074	-5232
chr11	40297086	40297150	E074	-4856
chr11	40297707	40297757	E074	-4249
chr11	40298313	40298384	E074	-3622
chr11	40298543	40298593	E074	-3413
chr11	40298631	40298847	E074	-3159
chr11	40299454	40299494	E074	-2512
chr11	40299703	40299763	E074	-2243
chr11	40299800	40299850	E074	-2156
chr11	40300136	40300186	E074	-1820
chr11	40306890	40306997	E074	4884
chr11	40307229	40307450	E074	5223
chr11	40307613	40307663	E074	5607
chr11	40307830	40307944	E074	5824
chr11	40307959	40308142	E074	5953
chr11	40308175	40308235	E074	6169
chr11	40308237	40308287	E074	6231
chr11	40308333	40308383	E074	6327
chr11	40350572	40351240	E074	48566
chr11	40290060	40290786	E081	-11220
chr11	40291038	40291078	E081	-10928
chr11	40301509	40301698	E081	-308
chr11	40301700	40303082	E081	0
chr11	40308572	40308625	E081	6566
chr11	40252539	40252677	E082	-49329
chr11	40291578	40291723	E082	-10283
chr11	40291804	40291877	E082	-10129
chr11	40292192	40292351	E082	-9655
chr11	40292528	40292578	E082	-9428
chr11	40301296	40301373	E082	-633

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr11	40309489	40309754	E067	7483
chr11	40309871	40309918	E067	7865
chr11	40310044	40310319	E067	8038
chr11	40310659	40310915	E067	8653
chr11	40311021	40311218	E067	9015
chr11	40311260	40311360	E067	9254
chr11	40311449	40311552	E067	9443
chr11	40311634	40312221	E067	9628
chr11	40312329	40312599	E067	10323
chr11	40312640	40312739	E067	10634
chr11	40312774	40312929	E067	10768
chr11	40312950	40313621	E067	10944
chr11	40313826	40314072	E067	11820
chr11	40314120	40315169	E067	12114
chr11	40315184	40316126	E067	13178
chr11	40309489	40309754	E068	7483
chr11	40309871	40309918	E068	7865
chr11	40310044	40310319	E068	8038
chr11	40310659	40310915	E068	8653
chr11	40311021	40311218	E068	9015
chr11	40311260	40311360	E068	9254
chr11	40311449	40311552	E068	9443
chr11	40311634	40312221	E068	9628
chr11	40312329	40312599	E068	10323
chr11	40312640	40312739	E068	10634
chr11	40312774	40312929	E068	10768
chr11	40312950	40313621	E068	10944
chr11	40313826	40314072	E068	11820
chr11	40314120	40315169	E068	12114
chr11	40315184	40316126	E068	13178
chr11	40309489	40309754	E069	7483
chr11	40309871	40309918	E069	7865
chr11	40310044	40310319	E069	8038
chr11	40310659	40310915	E069	8653
chr11	40311021	40311218	E069	9015
chr11	40311260	40311360	E069	9254
chr11	40311449	40311552	E069	9443
chr11	40311634	40312221	E069	9628
chr11	40312329	40312599	E069	10323
chr11	40312640	40312739	E069	10634
chr11	40312774	40312929	E069	10768
chr11	40312950	40313621	E069	10944
chr11	40313826	40314072	E069	11820
chr11	40314120	40315169	E069	12114
chr11	40315184	40316126	E069	13178
chr11	40311634	40312221	E070	9628
chr11	40312329	40312599	E070	10323
chr11	40312640	40312739	E070	10634
chr11	40312774	40312929	E070	10768
chr11	40312950	40313621	E070	10944
chr11	40313826	40314072	E070	11820
chr11	40314120	40315169	E070	12114
chr11	40315184	40316126	E070	13178
chr11	40309489	40309754	E071	7483
chr11	40309871	40309918	E071	7865
chr11	40310044	40310319	E071	8038
chr11	40310659	40310915	E071	8653
chr11	40311021	40311218	E071	9015
chr11	40311260	40311360	E071	9254
chr11	40311449	40311552	E071	9443
chr11	40311634	40312221	E071	9628
chr11	40312329	40312599	E071	10323
chr11	40312640	40312739	E071	10634
chr11	40312774	40312929	E071	10768
chr11	40312950	40313621	E071	10944
chr11	40313826	40314072	E071	11820
chr11	40314120	40315169	E071	12114
chr11	40315184	40316126	E071	13178
chr11	40309489	40309754	E072	7483
chr11	40309871	40309918	E072	7865
chr11	40310044	40310319	E072	8038
chr11	40310659	40310915	E072	8653
chr11	40311021	40311218	E072	9015
chr11	40311260	40311360	E072	9254
chr11	40311449	40311552	E072	9443
chr11	40311634	40312221	E072	9628
chr11	40312329	40312599	E072	10323
chr11	40312640	40312739	E072	10634
chr11	40312774	40312929	E072	10768
chr11	40312950	40313621	E072	10944
chr11	40313826	40314072	E072	11820
chr11	40314120	40315169	E072	12114
chr11	40315184	40316126	E072	13178
chr11	40309489	40309754	E073	7483
chr11	40309871	40309918	E073	7865
chr11	40310044	40310319	E073	8038
chr11	40310659	40310915	E073	8653
chr11	40311021	40311218	E073	9015
chr11	40311260	40311360	E073	9254
chr11	40311449	40311552	E073	9443
chr11	40311634	40312221	E073	9628
chr11	40312329	40312599	E073	10323
chr11	40312640	40312739	E073	10634
chr11	40312774	40312929	E073	10768
chr11	40312950	40313621	E073	10944
chr11	40313826	40314072	E073	11820
chr11	40314120	40315169	E073	12114
chr11	40315184	40316126	E073	13178
chr11	40309489	40309754	E074	7483
chr11	40309871	40309918	E074	7865
chr11	40310044	40310319	E074	8038
chr11	40310659	40310915	E074	8653
chr11	40311021	40311218	E074	9015
chr11	40311260	40311360	E074	9254
chr11	40311449	40311552	E074	9443
chr11	40311634	40312221	E074	9628
chr11	40312329	40312599	E074	10323
chr11	40312640	40312739	E074	10634
chr11	40312774	40312929	E074	10768
chr11	40312950	40313621	E074	10944
chr11	40313826	40314072	E074	11820
chr11	40314120	40315169	E074	12114
chr11	40315184	40316126	E074	13178
chr11	40309489	40309754	E081	7483
chr11	40309871	40309918	E081	7865
chr11	40310044	40310319	E081	8038
chr11	40310659	40310915	E081	8653
chr11	40311021	40311218	E081	9015
chr11	40311260	40311360	E081	9254
chr11	40311449	40311552	E081	9443
chr11	40311634	40312221	E081	9628
chr11	40312329	40312599	E081	10323
chr11	40312640	40312739	E081	10634
chr11	40312774	40312929	E081	10768
chr11	40312950	40313621	E081	10944
chr11	40313826	40314072	E081	11820
chr11	40314120	40315169	E081	12114
chr11	40309489	40309754	E082	7483
chr11	40309871	40309918	E082	7865
chr11	40310044	40310319	E082	8038
chr11	40310659	40310915	E082	8653
chr11	40311021	40311218	E082	9015
chr11	40311260	40311360	E082	9254
chr11	40311449	40311552	E082	9443
chr11	40311634	40312221	E082	9628
chr11	40312329	40312599	E082	10323
chr11	40312640	40312739	E082	10634
chr11	40312774	40312929	E082	10768
chr11	40312950	40313621	E082	10944
chr11	40313826	40314072	E082	11820
chr11	40314120	40315169	E082	12114
chr11	40315184	40316126	E082	13178