rs2372644

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

ANKS1B : Intron Variant
LOC101928937 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0340 (10210/29958,GnomAD)
G=0253 (7387/29118,TOPMED)
G=0381 (1908/5008,1000G)
G=0405 (1560/3854,ALSPAC)
G=0397 (1473/3708,TWINSUK)

Position: chr12:99096982 (GRCh38.p7) (12q23.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 109 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.99096982T>G
GRCh37.p13 chr 12	NC_000012.11:g.99490760T>G
ANKS1B RefSeqGene	NG_029860.1:g.892673A>C

Gene: ANKS1B, ankyrin repeat and sterile alpha motif domain containing 1B(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ANKS1B transcript variant 5	NM_001204066.1:c.	N/A	Intron Variant
ANKS1B transcript variant 6	NM_001204067.1:c.	N/A	Intron Variant
ANKS1B transcript variant 7	NM_001204068.1:c.	N/A	Intron Variant
ANKS1B transcript variant 8	NM_001204069.1:c.	N/A	Intron Variant
ANKS1B transcript variant 9	NM_001204070.1:c.	N/A	Intron Variant
ANKS1B transcript variant 3	NM_020140.3:c.	N/A	Intron Variant
ANKS1B transcript variant 1	NM_152788.4:c.	N/A	Intron Variant
ANKS1B transcript variant 2	NM_181670.3:c.	N/A	Intron Variant
ANKS1B transcript variant 4	NM_001204065.1:c.	N/A	Genic Upstream Transcript Variant
ANKS1B transcript variant 10	NM_001204079.1:c.	N/A	Genic Upstream Transcript Variant
ANKS1B transcript variant 11	NM_001204080.1:c.	N/A	Genic Upstream Transcript Variant
ANKS1B transcript variant 12	NM_001204081.1:c.	N/A	Genic Upstream Transcript Variant
ANKS1B transcript variant X9	XM_005269028.4:c.	N/A	Intron Variant
ANKS1B transcript variant X13	XM_005269029.4:c.	N/A	Intron Variant
ANKS1B transcript variant X2	XM_006719504.3:c.	N/A	Intron Variant
ANKS1B transcript variant X3	XM_006719505.3:c.	N/A	Intron Variant
ANKS1B transcript variant X4	XM_006719506.3:c.	N/A	Intron Variant
ANKS1B transcript variant X6	XM_006719507.3:c.	N/A	Intron Variant
ANKS1B transcript variant X10	XM_006719508.3:c.	N/A	Intron Variant
ANKS1B transcript variant X11	XM_006719509.3:c.	N/A	Intron Variant
ANKS1B transcript variant X16	XM_006719510.3:c.	N/A	Intron Variant
ANKS1B transcript variant X18	XM_006719512.3:c.	N/A	Intron Variant
ANKS1B transcript variant X19	XM_006719513.3:c.	N/A	Intron Variant
ANKS1B transcript variant X21	XM_006719514.3:c.	N/A	Intron Variant
ANKS1B transcript variant X14	XM_011538571.2:c.	N/A	Intron Variant
ANKS1B transcript variant X1	XM_017019651.1:c.	N/A	Intron Variant
ANKS1B transcript variant X5	XM_017019652.1:c.	N/A	Intron Variant
ANKS1B transcript variant X7	XM_017019653.1:c.	N/A	Intron Variant
ANKS1B transcript variant X8	XM_017019654.1:c.	N/A	Intron Variant
ANKS1B transcript variant X12	XM_017019655.1:c.	N/A	Intron Variant
ANKS1B transcript variant X15	XM_017019656.1:c.	N/A	Intron Variant
ANKS1B transcript variant X17	XM_017019657.1:c.	N/A	Intron Variant
ANKS1B transcript variant X20	XM_017019658.1:c.	N/A	Intron Variant
ANKS1B transcript variant X23	XM_017019659.1:c.	N/A	Intron Variant
ANKS1B transcript variant X24	XM_017019660.1:c.	N/A	Intron Variant
ANKS1B transcript variant X25	XM_017019661.1:c.	N/A	Intron Variant
ANKS1B transcript variant X26	XM_017019662.1:c.	N/A	Intron Variant
ANKS1B transcript variant X27	XM_017019663.1:c.	N/A	Intron Variant
ANKS1B transcript variant X28	XM_017019664.1:c.	N/A	Intron Variant
ANKS1B transcript variant X29	XM_017019665.1:c.	N/A	Intron Variant
ANKS1B transcript variant X30	XM_005269032.3:c.	N/A	Genic Upstream Transcript Variant
ANKS1B transcript variant X22	XR_001748815.1:n.	N/A	Intron Variant

Gene: LOC101928937, uncharacterized LOC101928937(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101928937 transcript	NR_110095.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.973	G=0.027
1000Genomes	American	Sub	694	T=0.470	G=0.530
1000Genomes	East Asian	Sub	1008	T=0.314	G=0.686
1000Genomes	Europe	Sub	1006	T=0.608	G=0.392
1000Genomes	Global	Study-wide	5008	T=0.619	G=0.381
1000Genomes	South Asian	Sub	978	T=0.570	G=0.430
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.595	G=0.405
The Genome Aggregation Database	African	Sub	8724	T=0.913	G=0.087
The Genome Aggregation Database	American	Sub	838	T=0.480	G=0.520
The Genome Aggregation Database	East Asian	Sub	1620	T=0.304	G=0.696
The Genome Aggregation Database	Europe	Sub	18474	T=0.579	G=0.421
The Genome Aggregation Database	Global	Study-wide	29958	T=0.659	G=0.340
The Genome Aggregation Database	Other	Sub	302	T=0.630	G=0.370
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.746	G=0.253
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.603	G=0.397

PMID	Title	Author	Journal
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
rs2372644	0.00068	alcohol dependence	24277619

eQTL of rs2372644 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 rs2372644 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 )
chr12	99453615	99453939	E067	-36821
chr12	99454003	99454097	E067	-36663
chr12	99454117	99454190	E067	-36570
chr12	99481054	99481411	E067	-9349
chr12	99481542	99481685	E067	-9075
chr12	99505857	99506040	E067	15097
chr12	99524722	99524838	E067	33962
chr12	99524932	99525071	E067	34172
chr12	99525092	99525207	E067	34332
chr12	99525252	99525317	E067	34492
chr12	99449245	99449289	E068	-41471
chr12	99481054	99481411	E068	-9349
chr12	99501653	99501870	E068	10893
chr12	99502008	99502058	E068	11248
chr12	99502093	99502143	E068	11333
chr12	99502685	99502750	E068	11925
chr12	99502751	99502805	E068	11991
chr12	99512694	99512777	E068	21934
chr12	99513459	99513509	E068	22699
chr12	99513964	99514083	E068	23204
chr12	99524421	99524525	E068	33661
chr12	99524722	99524838	E068	33962
chr12	99524932	99525071	E068	34172
chr12	99525092	99525207	E068	34332
chr12	99525252	99525317	E068	34492
chr12	99532026	99532076	E068	41266
chr12	99532147	99532203	E068	41387
chr12	99532247	99532469	E068	41487
chr12	99505857	99506040	E069	15097
chr12	99506164	99506214	E069	15404
chr12	99506343	99506403	E069	15583
chr12	99515218	99515671	E069	24458
chr12	99524722	99524838	E069	33962
chr12	99524932	99525071	E069	34172
chr12	99525092	99525207	E069	34332
chr12	99525252	99525317	E069	34492
chr12	99525380	99526251	E069	34620
chr12	99480764	99481022	E070	-9738
chr12	99481054	99481411	E070	-9349
chr12	99481542	99481685	E070	-9075
chr12	99481787	99481851	E070	-8909
chr12	99482073	99482124	E070	-8636
chr12	99504695	99504745	E070	13935
chr12	99504816	99504922	E070	14056
chr12	99505857	99506040	E070	15097
chr12	99515218	99515671	E070	24458
chr12	99516413	99516706	E070	25653
chr12	99524722	99524838	E070	33962
chr12	99524932	99525071	E070	34172
chr12	99525092	99525207	E070	34332
chr12	99525252	99525317	E070	34492
chr12	99525380	99526251	E070	34620
chr12	99532026	99532076	E070	41266
chr12	99532147	99532203	E070	41387
chr12	99532247	99532469	E070	41487
chr12	99532483	99532536	E070	41723
chr12	99536563	99536693	E070	45803
chr12	99524932	99525071	E071	34172
chr12	99525092	99525207	E071	34332
chr12	99525252	99525317	E071	34492
chr12	99525380	99526251	E071	34620
chr12	99515218	99515671	E072	24458
chr12	99524722	99524838	E072	33962
chr12	99524932	99525071	E072	34172
chr12	99525092	99525207	E072	34332
chr12	99525252	99525317	E072	34492
chr12	99525380	99526251	E072	34620
chr12	99455147	99455226	E073	-35534
chr12	99481054	99481411	E073	-9349
chr12	99504695	99504745	E073	13935
chr12	99504816	99504922	E073	14056
chr12	99443292	99443448	E081	-47312
chr12	99443728	99443819	E081	-46941
chr12	99443992	99444437	E081	-46323
chr12	99445362	99445490	E081	-45270
chr12	99460305	99460524	E081	-30236
chr12	99460593	99460803	E081	-29957
chr12	99460965	99461450	E081	-29310
chr12	99504155	99504258	E081	13395
chr12	99504440	99504508	E081	13680
chr12	99504695	99504745	E081	13935
chr12	99504816	99504922	E081	14056
chr12	99505857	99506040	E081	15097
chr12	99515218	99515671	E081	24458
chr12	99525092	99525207	E081	34332
chr12	99525252	99525317	E081	34492
chr12	99525380	99526251	E081	34620
chr12	99449245	99449289	E082	-41471
chr12	99450100	99450200	E082	-40560
chr12	99460305	99460524	E082	-30236
chr12	99460593	99460803	E082	-29957
chr12	99460965	99461450	E082	-29310
chr12	99481054	99481411	E082	-9349
chr12	99481542	99481685	E082	-9075
chr12	99481787	99481851	E082	-8909
chr12	99482073	99482124	E082	-8636
chr12	99504155	99504258	E082	13395
chr12	99504440	99504508	E082	13680
chr12	99504695	99504745	E082	13935
chr12	99504816	99504922	E082	14056
chr12	99505857	99506040	E082	15097
chr12	99515218	99515671	E082	24458
chr12	99516413	99516706	E082	25653
chr12	99524421	99524525	E082	33661
chr12	99524722	99524838	E082	33962
chr12	99524932	99525071	E082	34172
chr12	99525092	99525207	E082	34332
chr12	99525252	99525317	E082	34492
chr12	99525380	99526251	E082	34620