rs2001270

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

C1orf21 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0471 (14066/29850,GnomAD)
A==0467 (13613/29118,TOPMED)
G=0495 (2481/5008,1000G)
G=0394 (1519/3854,ALSPAC)
G=0399 (1480/3708,TWINSUK)

Position: chr1:184524750 (GRCh38.p7) (1q25.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 143 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.184524750A>G
GRCh37.p13 chr 1	NC_000001.10:g.184493884A>G

Gene: C1orf21, chromosome 1 open reading frame 21(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C1orf21 transcript	NM_030806.3:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.334	G=0.666
1000Genomes	American	Sub	694	A=0.480	G=0.520
1000Genomes	East Asian	Sub	1008	A=0.550	G=0.450
1000Genomes	Europe	Sub	1006	A=0.580	G=0.420
1000Genomes	Global	Study-wide	5008	A=0.505	G=0.495
1000Genomes	South Asian	Sub	978	A=0.630	G=0.370
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.606	G=0.394
The Genome Aggregation Database	African	Sub	8700	A=0.365	G=0.635
The Genome Aggregation Database	American	Sub	834	A=0.460	G=0.540
The Genome Aggregation Database	East Asian	Sub	1604	A=0.559	G=0.441
The Genome Aggregation Database	Europe	Sub	18410	A=0.606	G=0.393
The Genome Aggregation Database	Global	Study-wide	29850	A=0.528	G=0.471
The Genome Aggregation Database	Other	Sub	302	A=0.530	G=0.470
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.467	G=0.532
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.601	G=0.399

PMID	Title	Author	Journal
21529783	A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.	Heath AC	Biol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs2001270	0.0001	alcoholism (heaviness of drinking)	21529783

eQTL of rs2001270 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 rs2001270 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 )
chr1	184472590	184472671	E067	-21213
chr1	184472885	184472959	E067	-20925
chr1	184473024	184473179	E067	-20705
chr1	184476421	184476557	E067	-17327
chr1	184476648	184476698	E067	-17186
chr1	184476859	184477389	E067	-16495
chr1	184477599	184477649	E067	-16235
chr1	184477692	184477770	E067	-16114
chr1	184502306	184502473	E067	8422
chr1	184503161	184503325	E067	9277
chr1	184503348	184503454	E067	9464
chr1	184503795	184503845	E067	9911
chr1	184503951	184504219	E067	10067
chr1	184524577	184524642	E067	30693
chr1	184524837	184524895	E067	30953
chr1	184452103	184452816	E068	-41068
chr1	184459182	184459248	E068	-34636
chr1	184459358	184459702	E068	-34182
chr1	184472590	184472671	E068	-21213
chr1	184472885	184472959	E068	-20925
chr1	184473024	184473179	E068	-20705
chr1	184476421	184476557	E068	-17327
chr1	184476648	184476698	E068	-17186
chr1	184503161	184503325	E068	9277
chr1	184503348	184503454	E068	9464
chr1	184503795	184503845	E068	9911
chr1	184503951	184504219	E068	10067
chr1	184531274	184531822	E068	37390
chr1	184531868	184531966	E068	37984
chr1	184532019	184532338	E068	38135
chr1	184464116	184464193	E069	-29691
chr1	184472590	184472671	E069	-21213
chr1	184472885	184472959	E069	-20925
chr1	184473024	184473179	E069	-20705
chr1	184473507	184473802	E069	-20082
chr1	184487856	184488320	E069	-5564
chr1	184489616	184489733	E069	-4151
chr1	184503161	184503325	E069	9277
chr1	184503348	184503454	E069	9464
chr1	184524577	184524642	E069	30693
chr1	184524837	184524895	E069	30953
chr1	184466331	184466554	E070	-27330
chr1	184466555	184466684	E070	-27200
chr1	184466810	184466880	E070	-27004
chr1	184467147	184467490	E070	-26394
chr1	184472590	184472671	E070	-21213
chr1	184472885	184472959	E070	-20925
chr1	184473853	184474041	E070	-19843
chr1	184474187	184474290	E070	-19594
chr1	184487856	184488320	E070	-5564
chr1	184524577	184524642	E070	30693
chr1	184524837	184524895	E070	30953
chr1	184452103	184452816	E071	-41068
chr1	184457048	184457209	E071	-36675
chr1	184460745	184461804	E071	-32080
chr1	184472590	184472671	E071	-21213
chr1	184472885	184472959	E071	-20925
chr1	184473024	184473179	E071	-20705
chr1	184473507	184473802	E071	-20082
chr1	184473853	184474041	E071	-19843
chr1	184474187	184474290	E071	-19594
chr1	184476421	184476557	E071	-17327
chr1	184476648	184476698	E071	-17186
chr1	184503951	184504219	E071	10067
chr1	184504280	184504942	E071	10396
chr1	184524577	184524642	E071	30693
chr1	184524837	184524895	E071	30953
chr1	184524932	184525623	E071	31048
chr1	184454574	184454658	E072	-39226
chr1	184454786	184454836	E072	-39048
chr1	184454937	184455335	E072	-38549
chr1	184455379	184455746	E072	-38138
chr1	184466331	184466554	E072	-27330
chr1	184466555	184466684	E072	-27200
chr1	184473853	184474041	E072	-19843
chr1	184503161	184503325	E072	9277
chr1	184503348	184503454	E072	9464
chr1	184503795	184503845	E072	9911
chr1	184503951	184504219	E072	10067
chr1	184455379	184455746	E073	-38138
chr1	184455846	184456221	E073	-37663
chr1	184456237	184456418	E073	-37466
chr1	184456483	184456549	E073	-37335
chr1	184472885	184472959	E073	-20925
chr1	184473024	184473179	E073	-20705
chr1	184473507	184473802	E073	-20082
chr1	184473853	184474041	E073	-19843
chr1	184503161	184503325	E073	9277
chr1	184503348	184503454	E073	9464
chr1	184503795	184503845	E073	9911
chr1	184503951	184504219	E073	10067
chr1	184504280	184504942	E073	10396
chr1	184524577	184524642	E073	30693
chr1	184524837	184524895	E073	30953
chr1	184524932	184525623	E073	31048
chr1	184472590	184472671	E074	-21213
chr1	184472885	184472959	E074	-20925
chr1	184473024	184473179	E074	-20705
chr1	184474187	184474290	E074	-19594
chr1	184503161	184503325	E074	9277
chr1	184503348	184503454	E074	9464
chr1	184503795	184503845	E074	9911
chr1	184503951	184504219	E074	10067
chr1	184504280	184504942	E074	10396
chr1	184531274	184531822	E074	37390
chr1	184453664	184454116	E081	-39768
chr1	184454165	184454361	E081	-39523
chr1	184461822	184461971	E081	-31913
chr1	184461992	184462148	E081	-31736
chr1	184462326	184462379	E081	-31505
chr1	184462524	184462604	E081	-31280
chr1	184462607	184462738	E081	-31146
chr1	184462835	184462918	E081	-30966
chr1	184462958	184463464	E081	-30420
chr1	184465339	184465432	E081	-28452
chr1	184465688	184465745	E081	-28139
chr1	184466331	184466554	E081	-27330
chr1	184466555	184466684	E081	-27200
chr1	184466810	184466880	E081	-27004
chr1	184467147	184467490	E081	-26394
chr1	184473507	184473802	E081	-20082
chr1	184473853	184474041	E081	-19843
chr1	184474187	184474290	E081	-19594
chr1	184487856	184488320	E081	-5564
chr1	184516488	184516843	E081	22604
chr1	184517381	184517488	E081	23497
chr1	184524577	184524642	E081	30693
chr1	184524837	184524895	E081	30953
chr1	184453664	184454116	E082	-39768
chr1	184454937	184455335	E082	-38549
chr1	184455379	184455746	E082	-38138
chr1	184455846	184456221	E082	-37663
chr1	184456237	184456418	E082	-37466
chr1	184466331	184466554	E082	-27330
chr1	184466555	184466684	E082	-27200
chr1	184466810	184466880	E082	-27004
chr1	184467147	184467490	E082	-26394
chr1	184471483	184471574	E082	-22310
chr1	184472590	184472671	E082	-21213
chr1	184472885	184472959	E082	-20925
chr1	184474187	184474290	E082	-19594
chr1	184476859	184477389	E082	-16495
chr1	184487856	184488320	E082	-5564