rs10831759

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

MICAL2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0102 (3066/29936,GnomAD)
G=0114 (3333/29118,TOPMED)
G=0113 (566/5008,1000G)
G=0083 (318/3854,ALSPAC)
G=0081 (302/3708,TWINSUK)

Position: chr11:12199835 (GRCh38.p7) (11p15.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 324 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.12199835A>G
GRCh37.p13 chr 11	NC_000011.9:g.12221382A>G

Gene: MICAL2, microtubule associated monooxygenase, calponin and LIM domain containing 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MICAL2 transcript variant 2	NM_001282663.1:c.	N/A	Intron Variant
MICAL2 transcript variant 3	NM_001282664.1:c.	N/A	Intron Variant
MICAL2 transcript variant 4	NM_001282665.1:c.	N/A	Intron Variant
MICAL2 transcript variant 5	NM_001282666.1:c.	N/A	Intron Variant
MICAL2 transcript variant 6	NM_001282667.1:c.	N/A	Intron Variant
MICAL2 transcript variant 7	NM_001282668.1:c.	N/A	Intron Variant
MICAL2 transcript variant 1	NM_014632.3:c.	N/A	Intron Variant
MICAL2 transcript variant X1	XM_011520490.2:c.	N/A	Intron Variant
MICAL2 transcript variant X3	XM_011520491.2:c.	N/A	Intron Variant
MICAL2 transcript variant X4	XM_017018589.1:c.	N/A	Intron Variant
MICAL2 transcript variant X5	XM_017018590.1:c.	N/A	Intron Variant
MICAL2 transcript variant X6	XM_017018591.1:c.	N/A	Intron Variant
MICAL2 transcript variant X2	XR_001748049.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.823	G=0.177
1000Genomes	American	Sub	694	A=0.840	G=0.160
1000Genomes	East Asian	Sub	1008	A=0.907	G=0.093
1000Genomes	Europe	Sub	1006	A=0.903	G=0.097
1000Genomes	Global	Study-wide	5008	A=0.887	G=0.113
1000Genomes	South Asian	Sub	978	A=0.970	G=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.917	G=0.083
The Genome Aggregation Database	African	Sub	8702	A=0.848	G=0.152
The Genome Aggregation Database	American	Sub	838	A=0.840	G=0.160
The Genome Aggregation Database	East Asian	Sub	1620	A=0.895	G=0.105
The Genome Aggregation Database	Europe	Sub	18474	A=0.923	G=0.076
The Genome Aggregation Database	Global	Study-wide	29936	A=0.897	G=0.102
The Genome Aggregation Database	Other	Sub	302	A=0.920	G=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.885	G=0.114
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.919	G=0.081

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs10831759	4.48E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs10831759 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 rs10831759 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	12177566	12177616	E067	-43766
chr11	12177874	12177933	E067	-43449
chr11	12178037	12178077	E067	-43305
chr11	12178119	12178519	E067	-42863
chr11	12178528	12178679	E067	-42703
chr11	12179956	12180006	E067	-41376
chr11	12180200	12180405	E067	-40977
chr11	12180486	12181685	E067	-39697
chr11	12181696	12181993	E067	-39389
chr11	12182770	12183624	E067	-37758
chr11	12184238	12184292	E067	-37090
chr11	12184338	12184437	E067	-36945
chr11	12184575	12184648	E067	-36734
chr11	12184749	12186425	E067	-34957
chr11	12193866	12193956	E067	-27426
chr11	12194105	12194155	E067	-27227
chr11	12194196	12194307	E067	-27075
chr11	12207252	12207343	E067	-14039
chr11	12207380	12208116	E067	-13266
chr11	12241322	12241703	E067	19940
chr11	12241710	12242484	E067	20328
chr11	12242540	12242673	E067	21158
chr11	12242698	12242895	E067	21316
chr11	12242915	12243009	E067	21533
chr11	12243059	12243209	E067	21677
chr11	12243532	12244417	E067	22150
chr11	12264563	12266036	E067	43181
chr11	12266226	12266276	E067	44844
chr11	12266459	12266639	E067	45077
chr11	12266649	12266912	E067	45267
chr11	12267046	12267096	E067	45664
chr11	12267169	12267983	E067	45787
chr11	12267993	12268080	E067	46611
chr11	12268108	12268188	E067	46726
chr11	12268251	12268331	E067	46869
chr11	12268899	12269035	E067	47517
chr11	12269200	12269374	E067	47818
chr11	12269412	12270526	E067	48030
chr11	12270619	12270669	E067	49237
chr11	12270726	12270784	E067	49344
chr11	12270834	12270917	E067	49452
chr11	12178528	12178679	E068	-42703
chr11	12178719	12179581	E068	-41801
chr11	12180200	12180405	E068	-40977
chr11	12180486	12181685	E068	-39697
chr11	12181696	12181993	E068	-39389
chr11	12184749	12186425	E068	-34957
chr11	12237401	12239151	E068	16019
chr11	12241710	12242484	E068	20328
chr11	12242540	12242673	E068	21158
chr11	12242698	12242895	E068	21316
chr11	12242915	12243009	E068	21533
chr11	12243059	12243209	E068	21677
chr11	12268899	12269035	E068	47517
chr11	12269200	12269374	E068	47818
chr11	12269412	12270526	E068	48030
chr11	12270619	12270669	E068	49237
chr11	12270726	12270784	E068	49344
chr11	12270834	12270917	E068	49452
chr11	12172159	12173201	E069	-48181
chr11	12178037	12178077	E069	-43305
chr11	12178119	12178519	E069	-42863
chr11	12178528	12178679	E069	-42703
chr11	12178719	12179581	E069	-41801
chr11	12179618	12179754	E069	-41628
chr11	12179816	12179919	E069	-41463
chr11	12179956	12180006	E069	-41376
chr11	12180200	12180405	E069	-40977
chr11	12180486	12181685	E069	-39697
chr11	12181696	12181993	E069	-39389
chr11	12182097	12182181	E069	-39201
chr11	12182252	12182622	E069	-38760
chr11	12184575	12184648	E069	-36734
chr11	12184749	12186425	E069	-34957
chr11	12192201	12192286	E069	-29096
chr11	12192504	12193134	E069	-28248
chr11	12237401	12239151	E069	16019
chr11	12241710	12242484	E069	20328
chr11	12242540	12242673	E069	21158
chr11	12242698	12242895	E069	21316
chr11	12242915	12243009	E069	21533
chr11	12243059	12243209	E069	21677
chr11	12243532	12244417	E069	22150
chr11	12257007	12258546	E069	35625
chr11	12264563	12266036	E069	43181
chr11	12266226	12266276	E069	44844
chr11	12266459	12266639	E069	45077
chr11	12266649	12266912	E069	45267
chr11	12267046	12267096	E069	45664
chr11	12267169	12267983	E069	45787
chr11	12267993	12268080	E069	46611
chr11	12268108	12268188	E069	46726
chr11	12268251	12268331	E069	46869
chr11	12268899	12269035	E069	47517
chr11	12269200	12269374	E069	47818
chr11	12269412	12270526	E069	48030
chr11	12270619	12270669	E069	49237
chr11	12270726	12270784	E069	49344
chr11	12270834	12270917	E069	49452
chr11	12181696	12181993	E070	-39389
chr11	12182097	12182181	E070	-39201
chr11	12182252	12182622	E070	-38760
chr11	12241710	12242484	E070	20328
chr11	12242540	12242673	E070	21158
chr11	12242698	12242895	E070	21316
chr11	12242915	12243009	E070	21533
chr11	12262628	12262925	E070	41246
chr11	12263033	12263233	E070	41651
chr11	12263262	12263386	E070	41880
chr11	12263429	12264261	E070	42047
chr11	12264303	12264389	E070	42921
chr11	12264563	12266036	E070	43181
chr11	12266226	12266276	E070	44844
chr11	12266459	12266639	E070	45077
chr11	12266649	12266912	E070	45267
chr11	12267046	12267096	E070	45664
chr11	12267169	12267983	E070	45787
chr11	12269200	12269374	E070	47818
chr11	12269412	12270526	E070	48030
chr11	12270619	12270669	E070	49237
chr11	12270726	12270784	E070	49344
chr11	12270834	12270917	E070	49452
chr11	12178119	12178519	E071	-42863
chr11	12178528	12178679	E071	-42703
chr11	12180200	12180405	E071	-40977
chr11	12180486	12181685	E071	-39697
chr11	12181696	12181993	E071	-39389
chr11	12182097	12182181	E071	-39201
chr11	12182252	12182622	E071	-38760
chr11	12182770	12183624	E071	-37758
chr11	12184749	12186425	E071	-34957
chr11	12192504	12193134	E071	-28248
chr11	12203768	12205291	E071	-16091
chr11	12237401	12239151	E071	16019
chr11	12241710	12242484	E071	20328
chr11	12242540	12242673	E071	21158
chr11	12242698	12242895	E071	21316
chr11	12242915	12243009	E071	21533
chr11	12243059	12243209	E071	21677
chr11	12243532	12244417	E071	22150
chr11	12245084	12246723	E071	23702
chr11	12264563	12266036	E071	43181
chr11	12266226	12266276	E071	44844
chr11	12266459	12266639	E071	45077
chr11	12266649	12266912	E071	45267
chr11	12267046	12267096	E071	45664
chr11	12267169	12267983	E071	45787
chr11	12267993	12268080	E071	46611
chr11	12268108	12268188	E071	46726
chr11	12268251	12268331	E071	46869
chr11	12268899	12269035	E071	47517
chr11	12269200	12269374	E071	47818
chr11	12269412	12270526	E071	48030
chr11	12270619	12270669	E071	49237
chr11	12270726	12270784	E071	49344
chr11	12270834	12270917	E071	49452
chr11	12177874	12177933	E072	-43449
chr11	12178037	12178077	E072	-43305
chr11	12178119	12178519	E072	-42863
chr11	12178528	12178679	E072	-42703
chr11	12181696	12181993	E072	-39389
chr11	12182097	12182181	E072	-39201
chr11	12182252	12182622	E072	-38760
chr11	12182770	12183624	E072	-37758
chr11	12183672	12183994	E072	-37388
chr11	12184238	12184292	E072	-37090
chr11	12184338	12184437	E072	-36945
chr11	12184575	12184648	E072	-36734
chr11	12184749	12186425	E072	-34957
chr11	12186755	12187302	E072	-34080
chr11	12192201	12192286	E072	-29096
chr11	12192504	12193134	E072	-28248
chr11	12241710	12242484	E072	20328
chr11	12242540	12242673	E072	21158
chr11	12242698	12242895	E072	21316
chr11	12242915	12243009	E072	21533
chr11	12243059	12243209	E072	21677
chr11	12243532	12244417	E072	22150
chr11	12264563	12266036	E072	43181
chr11	12266226	12266276	E072	44844
chr11	12266459	12266639	E072	45077
chr11	12266649	12266912	E072	45267
chr11	12267046	12267096	E072	45664
chr11	12267169	12267983	E072	45787
chr11	12267993	12268080	E072	46611
chr11	12268108	12268188	E072	46726
chr11	12268251	12268331	E072	46869
chr11	12268899	12269035	E072	47517
chr11	12269200	12269374	E072	47818
chr11	12269412	12270526	E072	48030
chr11	12270619	12270669	E072	49237
chr11	12270726	12270784	E072	49344
chr11	12270834	12270917	E072	49452
chr11	12173225	12173287	E073	-48095
chr11	12173385	12173465	E073	-47917
chr11	12177566	12177616	E073	-43766
chr11	12177874	12177933	E073	-43449
chr11	12178037	12178077	E073	-43305
chr11	12178119	12178519	E073	-42863
chr11	12178528	12178679	E073	-42703
chr11	12180200	12180405	E073	-40977
chr11	12180486	12181685	E073	-39697
chr11	12181696	12181993	E073	-39389
chr11	12182097	12182181	E073	-39201
chr11	12182252	12182622	E073	-38760
chr11	12182770	12183624	E073	-37758
chr11	12183672	12183994	E073	-37388
chr11	12184238	12184292	E073	-37090
chr11	12184338	12184437	E073	-36945
chr11	12184575	12184648	E073	-36734
chr11	12184749	12186425	E073	-34957
chr11	12186755	12187302	E073	-34080
chr11	12200379	12200436	E073	-20946
chr11	12200465	12201834	E073	-19548
chr11	12206648	12206750	E073	-14632
chr11	12206753	12206860	E073	-14522
chr11	12206904	12206989	E073	-14393
chr11	12207005	12207163	E073	-14219
chr11	12207252	12207343	E073	-14039
chr11	12207380	12208116	E073	-13266
chr11	12208170	12208220	E073	-13162
chr11	12220081	12220161	E073	-1221
chr11	12241710	12242484	E073	20328
chr11	12242540	12242673	E073	21158
chr11	12242698	12242895	E073	21316
chr11	12242915	12243009	E073	21533
chr11	12243059	12243209	E073	21677
chr11	12243532	12244417	E073	22150
chr11	12254261	12254880	E073	32879
chr11	12254893	12255164	E073	33511
chr11	12256788	12256952	E073	35406
chr11	12257007	12258546	E073	35625
chr11	12263429	12264261	E073	42047
chr11	12264303	12264389	E073	42921
chr11	12264563	12266036	E073	43181
chr11	12266226	12266276	E073	44844
chr11	12266459	12266639	E073	45077
chr11	12266649	12266912	E073	45267
chr11	12267046	12267096	E073	45664
chr11	12268899	12269035	E073	47517
chr11	12269200	12269374	E073	47818
chr11	12180200	12180405	E074	-40977
chr11	12180486	12181685	E074	-39697
chr11	12181696	12181993	E074	-39389
chr11	12182097	12182181	E074	-39201
chr11	12182252	12182622	E074	-38760
chr11	12182770	12183624	E074	-37758
chr11	12184238	12184292	E074	-37090
chr11	12184338	12184437	E074	-36945
chr11	12184575	12184648	E074	-36734
chr11	12184749	12186425	E074	-34957
chr11	12192201	12192286	E074	-29096
chr11	12241710	12242484	E074	20328
chr11	12242540	12242673	E074	21158
chr11	12242698	12242895	E074	21316
chr11	12242915	12243009	E074	21533
chr11	12243059	12243209	E074	21677
chr11	12243532	12244417	E074	22150
chr11	12268108	12268188	E074	46726
chr11	12268899	12269035	E074	47517
chr11	12269200	12269374	E074	47818
chr11	12269412	12270526	E074	48030
chr11	12270619	12270669	E074	49237
chr11	12270726	12270784	E074	49344
chr11	12270834	12270917	E074	49452
chr11	12180200	12180405	E081	-40977
chr11	12180486	12181685	E081	-39697
chr11	12181696	12181993	E081	-39389
chr11	12182097	12182181	E081	-39201
chr11	12182252	12182622	E081	-38760
chr11	12186755	12187302	E081	-34080
chr11	12189615	12189763	E081	-31619
chr11	12189795	12189958	E081	-31424
chr11	12235416	12235529	E081	14034
chr11	12235550	12235903	E081	14168
chr11	12235931	12236032	E081	14549
chr11	12236259	12237378	E081	14877
chr11	12237401	12239151	E081	16019
chr11	12239182	12239397	E081	17800
chr11	12239491	12239572	E081	18109
chr11	12239634	12239720	E081	18252
chr11	12239821	12240012	E081	18439
chr11	12240118	12240168	E081	18736
chr11	12240249	12240349	E081	18867
chr11	12240426	12240940	E081	19044
chr11	12241076	12241249	E081	19694
chr11	12241322	12241703	E081	19940
chr11	12241710	12242484	E081	20328
chr11	12242540	12242673	E081	21158
chr11	12242698	12242895	E081	21316
chr11	12242915	12243009	E081	21533
chr11	12243059	12243209	E081	21677
chr11	12255743	12255815	E081	34361
chr11	12255897	12256093	E081	34515
chr11	12256105	12256453	E081	34723
chr11	12256788	12256952	E081	35406
chr11	12263429	12264261	E081	42047
chr11	12264303	12264389	E081	42921
chr11	12264563	12266036	E081	43181
chr11	12266226	12266276	E081	44844
chr11	12266459	12266639	E081	45077
chr11	12266649	12266912	E081	45267
chr11	12267046	12267096	E081	45664
chr11	12267169	12267983	E081	45787
chr11	12267993	12268080	E081	46611
chr11	12268108	12268188	E081	46726
chr11	12180486	12181685	E082	-39697
chr11	12181696	12181993	E082	-39389
chr11	12236259	12237378	E082	14877
chr11	12237401	12239151	E082	16019
chr11	12239182	12239397	E082	17800
chr11	12241322	12241703	E082	19940
chr11	12241710	12242484	E082	20328
chr11	12263429	12264261	E082	42047
chr11	12264303	12264389	E082	42921
chr11	12264563	12266036	E082	43181
chr11	12266226	12266276	E082	44844
chr11	12266459	12266639	E082	45077
chr11	12266649	12266912	E082	45267
chr11	12267046	12267096	E082	45664
chr11	12267169	12267983	E082	45787
chr11	12270619	12270669	E082	49237
chr11	12270726	12270784	E082	49344
chr11	12270834	12270917	E082	49452