rs10877015

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

METTL21B : Intron Variant
METTL1 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0287 (8596/29926,GnomAD)
G=0238 (6930/29118,TOPMED)
G=0354 (1775/5008,1000G)
G=0328 (1265/3854,ALSPAC)
G=0301 (1117/3708,TWINSUK)

Position: chr12:57774005 (GRCh38.p7) (12q14.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 197 Enhancers around

Promoter: 86 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.57774005A>G
GRCh37.p13 chr 12	NC_000012.11:g.58167788A>G

Gene: METTL21B, methyltransferase like 21B(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EEF1AKMT3 transcript variant 1	NM_015433.2:c.	N/A	Intron Variant
EEF1AKMT3 transcript variant 2	NM_206914.1:c.	N/A	Intron Variant

Gene: METTL1, methyltransferase like 1(minus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
METTL1 transcript variant 1	NM_005371.5:c.	N/A	Upstream Transcript Variant
METTL1 transcript variant 3	NM_023033.3:c.	N/A	Upstream Transcript Variant
METTL1 transcript variant X1	XM_005268873.2:c.	N/A	Upstream Transcript Variant
METTL1 transcript variant X2	XM_017019305.1:c.	N/A	Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.910	G=0.090
1000Genomes	American	Sub	694	A=0.740	G=0.260
1000Genomes	East Asian	Sub	1008	A=0.355	G=0.645
1000Genomes	Europe	Sub	1006	A=0.682	G=0.318
1000Genomes	Global	Study-wide	5008	A=0.646	G=0.354
1000Genomes	South Asian	Sub	978	A=0.480	G=0.520
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.672	G=0.328
The Genome Aggregation Database	African	Sub	8716	A=0.862	G=0.138
The Genome Aggregation Database	American	Sub	838	A=0.670	G=0.330
The Genome Aggregation Database	East Asian	Sub	1618	A=0.374	G=0.626
The Genome Aggregation Database	Europe	Sub	18454	A=0.673	G=0.326
The Genome Aggregation Database	Global	Study-wide	29926	A=0.712	G=0.287
The Genome Aggregation Database	Other	Sub	300	A=0.700	G=0.300
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.762	G=0.238
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.699	G=0.301

PMID	Title	Author	Journal
23160276	Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis.	Alcina A	J Med Genet
20648053	Confirmation of association between multiple sclerosis and CYP27B1.	Sundqvist E	Eur J Hum Genet
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs10877015	0.00046	alcohol dependence	24277619

eQTL of rs10877015 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	1.0000e-28	2399	Cerebellum
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	1.4427e-11	2399	Frontal_Cortex_BA9
Chr12:58167788	TSFM	ENSG00000123297.12	A>G	8.5703e-8	-8584	Frontal_Cortex_BA9
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	8.9850e-12	2399	Hypothalamus
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	3.7802e-16	2399	Cortex
Chr12:58167788	TSFM	ENSG00000123297.12	A>G	1.2549e-2	-8584	Cortex
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	1.1150e-25	2399	Cerebellar_Hemisphere
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	4.7754e-16	2399	Caudate_basal_ganglia
Chr12:58167788	TSFM	ENSG00000123297.12	A>G	2.4810e-5	-8584	Caudate_basal_ganglia
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	6.4426e-9	2399	Brain_Spinal_cord_cervical
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	1.1802e-8	2399	Hippocampus
Chr12:58167788	TSFM	ENSG00000123297.12	A>G	2.9600e-4	-8584	Hippocampus
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	2.2657e-14	2399	Putamen_basal_ganglia
Chr12:58167788	TSFM	ENSG00000123297.12	A>G	1.0905e-3	-8584	Putamen_basal_ganglia
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	2.2169e-7	2399	Anterior_cingulate_cortex
Chr12:58167788	TSFM	ENSG00000123297.12	A>G	7.2621e-4	-8584	Anterior_cingulate_cortex
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	5.8419e-18	2399	Nucleus_accumbens_basal_ganglia
Chr12:58167788	TSFM	ENSG00000123297.12	A>G	4.3429e-4	-8584	Nucleus_accumbens_basal_ganglia
Chr12:58167788	METTL21B	ENSG00000123427.11	A>G	1.2202e-6	2399	Amygdala

meQTL of rs10877015 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg04478727	chr12:58166393	METTL1\|FAM119B	0.00441148825557052	2.1134e-14
cg04478727	chr12:58166393	METTL1\|FAM119B	0.004411488	2.1100e-14

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 )
chr12	58177659	58177810	E067	9871
chr12	58177857	58177931	E067	10069
chr12	58178106	58178164	E067	10318
chr12	58207397	58207494	E067	39609
chr12	58207850	58207904	E067	40062
chr12	58207922	58207972	E067	40134
chr12	58208078	58208252	E067	40290
chr12	58208254	58208659	E067	40466
chr12	58209020	58209246	E067	41232
chr12	58209399	58209532	E067	41611
chr12	58209535	58209607	E067	41747
chr12	58209620	58209721	E067	41832
chr12	58209772	58209835	E067	41984
chr12	58209844	58210056	E067	42056
chr12	58210185	58210325	E067	42397
chr12	58210397	58210469	E067	42609
chr12	58210570	58210833	E067	42782
chr12	58210841	58210863	E067	43053
chr12	58210920	58210972	E067	43132
chr12	58211102	58211459	E067	43314
chr12	58126403	58126488	E068	-41300
chr12	58126556	58126613	E068	-41175
chr12	58126624	58126759	E068	-41029
chr12	58126836	58126886	E068	-40902
chr12	58126930	58127030	E068	-40758
chr12	58127058	58127179	E068	-40609
chr12	58127242	58127353	E068	-40435
chr12	58127418	58127468	E068	-40320
chr12	58127472	58127552	E068	-40236
chr12	58127588	58127674	E068	-40114
chr12	58127799	58127873	E068	-39915
chr12	58128028	58128090	E068	-39698
chr12	58128169	58128323	E068	-39465
chr12	58128363	58128537	E068	-39251
chr12	58128564	58128731	E068	-39057
chr12	58128788	58128911	E068	-38877
chr12	58147094	58147433	E068	-20355
chr12	58147455	58147565	E068	-20223
chr12	58147607	58147720	E068	-20068
chr12	58197099	58197594	E068	29311
chr12	58207850	58207904	E068	40062
chr12	58207922	58207972	E068	40134
chr12	58208078	58208252	E068	40290
chr12	58208254	58208659	E068	40466
chr12	58209399	58209532	E068	41611
chr12	58209535	58209607	E068	41747
chr12	58209620	58209721	E068	41832
chr12	58209772	58209835	E068	41984
chr12	58209844	58210056	E068	42056
chr12	58210185	58210325	E068	42397
chr12	58210397	58210469	E068	42609
chr12	58210570	58210833	E068	42782
chr12	58210841	58210863	E068	43053
chr12	58210920	58210972	E068	43132
chr12	58211102	58211459	E068	43314
chr12	58211502	58211820	E068	43714
chr12	58211856	58211960	E068	44068
chr12	58212135	58212206	E068	44347
chr12	58212266	58212395	E068	44478
chr12	58212469	58212634	E068	44681
chr12	58212677	58213094	E068	44889
chr12	58215039	58215097	E068	47251
chr12	58215176	58215264	E068	47388
chr12	58215405	58215570	E068	47617
chr12	58215628	58215728	E068	47840
chr12	58215843	58215894	E068	48055
chr12	58216130	58216401	E068	48342
chr12	58216502	58216813	E068	48714
chr12	58133671	58133951	E069	-33837
chr12	58133972	58134016	E069	-33772
chr12	58175721	58175850	E069	7933
chr12	58177659	58177810	E069	9871
chr12	58177857	58177931	E069	10069
chr12	58207850	58207904	E069	40062
chr12	58207922	58207972	E069	40134
chr12	58208078	58208252	E069	40290
chr12	58208254	58208659	E069	40466
chr12	58210841	58210863	E069	43053
chr12	58210920	58210972	E069	43132
chr12	58211102	58211459	E069	43314
chr12	58119120	58119363	E070	-48425
chr12	58119383	58119433	E070	-48355
chr12	58119453	58119497	E070	-48291
chr12	58119536	58119590	E070	-48198
chr12	58142859	58142917	E070	-24871
chr12	58142997	58143108	E070	-24680
chr12	58143175	58143285	E070	-24503
chr12	58177659	58177810	E070	9871
chr12	58177857	58177931	E070	10069
chr12	58126836	58126886	E071	-40902
chr12	58126930	58127030	E071	-40758
chr12	58140104	58140227	E071	-27561
chr12	58144186	58144240	E071	-23548
chr12	58177659	58177810	E071	9871
chr12	58177857	58177931	E071	10069
chr12	58208078	58208252	E071	40290
chr12	58208254	58208659	E071	40466
chr12	58209535	58209607	E071	41747
chr12	58209620	58209721	E071	41832
chr12	58209772	58209835	E071	41984
chr12	58209844	58210056	E071	42056
chr12	58210185	58210325	E071	42397
chr12	58210397	58210469	E071	42609
chr12	58210570	58210833	E071	42782
chr12	58210841	58210863	E071	43053
chr12	58210920	58210972	E071	43132
chr12	58133671	58133951	E072	-33837
chr12	58137782	58137863	E072	-29925
chr12	58167430	58167542	E072	-246
chr12	58177659	58177810	E072	9871
chr12	58177857	58177931	E072	10069
chr12	58178106	58178164	E072	10318
chr12	58197099	58197594	E072	29311
chr12	58206581	58206641	E072	38793
chr12	58206751	58206808	E072	38963
chr12	58206817	58206924	E072	39029
chr12	58207006	58207186	E072	39218
chr12	58207397	58207494	E072	39609
chr12	58207850	58207904	E072	40062
chr12	58207922	58207972	E072	40134
chr12	58208078	58208252	E072	40290
chr12	58208254	58208659	E072	40466
chr12	58209020	58209246	E072	41232
chr12	58209399	58209532	E072	41611
chr12	58209535	58209607	E072	41747
chr12	58209620	58209721	E072	41832
chr12	58209772	58209835	E072	41984
chr12	58209844	58210056	E072	42056
chr12	58210185	58210325	E072	42397
chr12	58210397	58210469	E072	42609
chr12	58210570	58210833	E072	42782
chr12	58210841	58210863	E072	43053
chr12	58210920	58210972	E072	43132
chr12	58211102	58211459	E072	43314
chr12	58211502	58211820	E072	43714
chr12	58127242	58127353	E073	-40435
chr12	58128169	58128323	E073	-39465
chr12	58128363	58128537	E073	-39251
chr12	58128564	58128731	E073	-39057
chr12	58128788	58128911	E073	-38877
chr12	58133671	58133951	E073	-33837
chr12	58133972	58134016	E073	-33772
chr12	58140104	58140227	E073	-27561
chr12	58140344	58140436	E073	-27352
chr12	58177659	58177810	E073	9871
chr12	58177857	58177931	E073	10069
chr12	58207850	58207904	E073	40062
chr12	58207922	58207972	E073	40134
chr12	58208078	58208252	E073	40290
chr12	58208254	58208659	E073	40466
chr12	58209020	58209246	E073	41232
chr12	58209399	58209532	E073	41611
chr12	58209535	58209607	E073	41747
chr12	58209620	58209721	E073	41832
chr12	58209772	58209835	E073	41984
chr12	58209844	58210056	E073	42056
chr12	58210185	58210325	E073	42397
chr12	58210397	58210469	E073	42609
chr12	58210570	58210833	E073	42782
chr12	58210841	58210863	E073	43053
chr12	58210920	58210972	E073	43132
chr12	58211102	58211459	E073	43314
chr12	58211502	58211820	E073	43714
chr12	58177659	58177810	E074	9871
chr12	58177857	58177931	E074	10069
chr12	58178106	58178164	E074	10318
chr12	58209535	58209607	E074	41747
chr12	58209620	58209721	E074	41832
chr12	58209772	58209835	E074	41984
chr12	58209844	58210056	E074	42056
chr12	58210185	58210325	E074	42397
chr12	58210397	58210469	E074	42609
chr12	58210570	58210833	E074	42782
chr12	58210841	58210863	E074	43053
chr12	58210920	58210972	E074	43132
chr12	58211102	58211459	E074	43314
chr12	58211502	58211820	E074	43714
chr12	58212135	58212206	E074	44347
chr12	58212266	58212395	E074	44478
chr12	58212469	58212634	E074	44681
chr12	58212677	58213094	E074	44889
chr12	58133671	58133951	E081	-33837
chr12	58144093	58144145	E081	-23643
chr12	58144186	58144240	E081	-23548
chr12	58147094	58147433	E081	-20355
chr12	58147455	58147565	E081	-20223
chr12	58147607	58147720	E081	-20068
chr12	58167430	58167542	E081	-246
chr12	58133671	58133951	E082	-33837
chr12	58137782	58137863	E082	-29925
chr12	58140104	58140227	E082	-27561
chr12	58177659	58177810	E082	9871
chr12	58177857	58177931	E082	10069
chr12	58178106	58178164	E082	10318
chr12	58210841	58210863	E082	43053
chr12	58210920	58210972	E082	43132
chr12	58211102	58211459	E082	43314

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	58119723	58121936	E067	-45852
chr12	58129081	58131250	E067	-36538
chr12	58131271	58131336	E067	-36452
chr12	58131351	58131680	E067	-36108
chr12	58131698	58132243	E067	-35545
chr12	58132333	58133623	E067	-34165
chr12	58137866	58140086	E067	-27702
chr12	58144309	58147042	E067	-20746
chr12	58147741	58149530	E067	-18258
chr12	58165006	58167168	E067	-620
chr12	58175890	58177381	E067	8102
chr12	58119723	58121936	E068	-45852
chr12	58129081	58131250	E068	-36538
chr12	58131271	58131336	E068	-36452
chr12	58131351	58131680	E068	-36108
chr12	58131698	58132243	E068	-35545
chr12	58132333	58133623	E068	-34165
chr12	58137866	58140086	E068	-27702
chr12	58144309	58147042	E068	-20746
chr12	58147741	58149530	E068	-18258
chr12	58165006	58167168	E068	-620
chr12	58175890	58177381	E068	8102
chr12	58119610	58119705	E069	-48083
chr12	58119723	58121936	E069	-45852
chr12	58131351	58131680	E069	-36108
chr12	58131698	58132243	E069	-35545
chr12	58132333	58133623	E069	-34165
chr12	58137866	58140086	E069	-27702
chr12	58144309	58147042	E069	-20746
chr12	58147741	58149530	E069	-18258
chr12	58165006	58167168	E069	-620
chr12	58175890	58177381	E069	8102
chr12	58131698	58132243	E070	-35545
chr12	58137866	58140086	E070	-27702
chr12	58144309	58147042	E070	-20746
chr12	58147741	58149530	E070	-18258
chr12	58165006	58167168	E070	-620
chr12	58175890	58177381	E070	8102
chr12	58119723	58121936	E071	-45852
chr12	58137866	58140086	E071	-27702
chr12	58144309	58147042	E071	-20746
chr12	58147741	58149530	E071	-18258
chr12	58165006	58167168	E071	-620
chr12	58175890	58177381	E071	8102
chr12	58119723	58121936	E072	-45852
chr12	58131351	58131680	E072	-36108
chr12	58131698	58132243	E072	-35545
chr12	58132333	58133623	E072	-34165
chr12	58137866	58140086	E072	-27702
chr12	58144309	58147042	E072	-20746
chr12	58147741	58149530	E072	-18258
chr12	58158277	58161295	E072	-6493
chr12	58165006	58167168	E072	-620
chr12	58175890	58177381	E072	8102
chr12	58119610	58119705	E073	-48083
chr12	58119723	58121936	E073	-45852
chr12	58129081	58131250	E073	-36538
chr12	58131271	58131336	E073	-36452
chr12	58131351	58131680	E073	-36108
chr12	58131698	58132243	E073	-35545
chr12	58132333	58133623	E073	-34165
chr12	58137866	58140086	E073	-27702
chr12	58144309	58147042	E073	-20746
chr12	58147741	58149530	E073	-18258
chr12	58165006	58167168	E073	-620
chr12	58175890	58177381	E073	8102
chr12	58119723	58121936	E074	-45852
chr12	58137866	58140086	E074	-27702
chr12	58144309	58147042	E074	-20746
chr12	58147741	58149530	E074	-18258
chr12	58165006	58167168	E074	-620
chr12	58175890	58177381	E074	8102
chr12	58137866	58140086	E081	-27702
chr12	58144309	58147042	E081	-20746
chr12	58147741	58149530	E081	-18258
chr12	58165006	58167168	E081	-620
chr12	58119610	58119705	E082	-48083
chr12	58119723	58121936	E082	-45852
chr12	58131271	58131336	E082	-36452
chr12	58131351	58131680	E082	-36108
chr12	58131698	58132243	E082	-35545
chr12	58137866	58140086	E082	-27702
chr12	58144309	58147042	E082	-20746
chr12	58147741	58149530	E082	-18258
chr12	58165006	58167168	E082	-620
chr12	58175890	58177381	E082	8102