rs11121671

Organism: Homo sapiens

Alleles: C>A / C>T

Gene : Feature

C1orf127 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0276 (8235/29746,GnomAD)
T=0317 (9236/29118,TOPMED)
T=0238 (1191/5008,1000G)
T=0204 (787/3854,ALSPAC)
T=0189 (702/3708,TWINSUK)

Position: chr1:10983723 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 45 Enhancers around

Promoter: 120 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.10983723C>A
GRCh38.p7 chr 1	NC_000001.11:g.10983723C>T
GRCh37.p13 chr 1	NC_000001.10:g.11043780C>A
GRCh37.p13 chr 1	NC_000001.10:g.11043780C>T

Gene: C1orf127, chromosome 1 open reading frame 127(minus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
C1orf127 transcript	NM_001170754.1:c.	N/A	Upstream Transcript Variant
C1orf127 transcript variant X1	XM_017000373.1:c.	N/A	N/A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.470	A=0.006
1000Genomes	American	Sub	694	C=0.830	A=0.00,
1000Genomes	East Asian	Sub	1008	C=0.921	A=0.000
1000Genomes	Europe	Sub	1006	C=0.798	A=0.000
1000Genomes	Global	Study-wide	5008	C=0.761	A=0.002
1000Genomes	South Asian	Sub	978	C=0.900	A=0.00,
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.796	T=0.204
The Genome Aggregation Database	African	Sub	8676	C=0.534	T=0.465
The Genome Aggregation Database	American	Sub	836	C=0.860	T=0.14,
The Genome Aggregation Database	East Asian	Sub	1606	C=0.928	T=0.072
The Genome Aggregation Database	Europe	Sub	18326	C=0.786	T=0.213
The Genome Aggregation Database	Global	Study-wide	29746	C=0.722	T=0.276
The Genome Aggregation Database	Other	Sub	302	C=0.770	T=0.23,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.682	T=0.317
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.811	T=0.189

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
rs11121671	0.000448	alcohol dependence	24277619

eQTL of rs11121671 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 rs11121671 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	177112269	177112312	E067	-744
chr1	177072371	177072502	E068	-40554
chr1	177088601	177088662	E068	-24394
chr1	177103834	177103884	E068	-9172
chr1	177104346	177104390	E068	-8666
chr1	177106441	177106652	E068	-6404
chr1	177106767	177106854	E068	-6202
chr1	177130970	177131030	E068	17914
chr1	177151478	177151704	E068	38422
chr1	177072371	177072502	E069	-40554
chr1	177086236	177086276	E069	-26780
chr1	177088601	177088662	E069	-24394
chr1	177107530	177107574	E069	-5482
chr1	177130970	177131030	E069	17914
chr1	177072371	177072502	E070	-40554
chr1	177151478	177151704	E070	38422
chr1	177088601	177088662	E071	-24394
chr1	177130970	177131030	E071	17914
chr1	177139205	177139335	E071	26149
chr1	177151478	177151704	E071	38422
chr1	177159831	177159964	E071	46775
chr1	177072371	177072502	E072	-40554
chr1	177104346	177104390	E072	-8666
chr1	177151478	177151704	E072	38422
chr1	177072371	177072502	E073	-40554
chr1	177088601	177088662	E073	-24394
chr1	177091340	177091390	E073	-21666
chr1	177091533	177091578	E073	-21478
chr1	177091728	177091853	E073	-21203
chr1	177092026	177092277	E073	-20779
chr1	177104346	177104390	E073	-8666
chr1	177107092	177107251	E073	-5805
chr1	177151478	177151704	E073	38422
chr1	177152266	177152604	E073	39210
chr1	177130970	177131030	E074	17914
chr1	177139205	177139335	E074	26149
chr1	177072371	177072502	E081	-40554
chr1	177088601	177088662	E081	-24394
chr1	177127636	177127692	E081	14580
chr1	177130970	177131030	E081	17914
chr1	177151478	177151704	E081	38422
chr1	177152266	177152604	E081	39210
chr1	177159311	177159743	E081	46255
chr1	177088601	177088662	E082	-24394
chr1	177159311	177159743	E082	46255

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	177131509	177131626	E067	18453
chr1	177132857	177132907	E067	19801
chr1	177132999	177134316	E067	19943
chr1	177139645	177139788	E067	26589
chr1	177139847	177140904	E067	26791
chr1	177141013	177141128	E067	27957
chr1	177141265	177141352	E067	28209
chr1	177141410	177141496	E067	28354
chr1	177141587	177141669	E067	28531
chr1	177141817	177141886	E067	28761
chr1	177142156	177142232	E067	29100
chr1	177142487	177142602	E067	29431
chr1	177150351	177150449	E067	37295
chr1	177150590	177151420	E067	37534
chr1	177131509	177131626	E068	18453
chr1	177132857	177132907	E068	19801
chr1	177132999	177134316	E068	19943
chr1	177139645	177139788	E068	26589
chr1	177139847	177140904	E068	26791
chr1	177141013	177141128	E068	27957
chr1	177141265	177141352	E068	28209
chr1	177141410	177141496	E068	28354
chr1	177141587	177141669	E068	28531
chr1	177142156	177142232	E068	29100
chr1	177150351	177150449	E068	37295
chr1	177150590	177151420	E068	37534
chr1	177131509	177131626	E069	18453
chr1	177132857	177132907	E069	19801
chr1	177132999	177134316	E069	19943
chr1	177139645	177139788	E069	26589
chr1	177139847	177140904	E069	26791
chr1	177141013	177141128	E069	27957
chr1	177141265	177141352	E069	28209
chr1	177141410	177141496	E069	28354
chr1	177141587	177141669	E069	28531
chr1	177141817	177141886	E069	28761
chr1	177142156	177142232	E069	29100
chr1	177142487	177142602	E069	29431
chr1	177150590	177151420	E069	37534
chr1	177131509	177131626	E070	18453
chr1	177132857	177132907	E070	19801
chr1	177132999	177134316	E070	19943
chr1	177139847	177140904	E070	26791
chr1	177141013	177141128	E070	27957
chr1	177141265	177141352	E070	28209
chr1	177141410	177141496	E070	28354
chr1	177141587	177141669	E070	28531
chr1	177142487	177142602	E070	29431
chr1	177150351	177150449	E070	37295
chr1	177150590	177151420	E070	37534
chr1	177131509	177131626	E071	18453
chr1	177132857	177132907	E071	19801
chr1	177132999	177134316	E071	19943
chr1	177139645	177139788	E071	26589
chr1	177139847	177140904	E071	26791
chr1	177141013	177141128	E071	27957
chr1	177141265	177141352	E071	28209
chr1	177141410	177141496	E071	28354
chr1	177141587	177141669	E071	28531
chr1	177141817	177141886	E071	28761
chr1	177142156	177142232	E071	29100
chr1	177142487	177142602	E071	29431
chr1	177150351	177150449	E071	37295
chr1	177150590	177151420	E071	37534
chr1	177131509	177131626	E072	18453
chr1	177132857	177132907	E072	19801
chr1	177132999	177134316	E072	19943
chr1	177139645	177139788	E072	26589
chr1	177139847	177140904	E072	26791
chr1	177141013	177141128	E072	27957
chr1	177141265	177141352	E072	28209
chr1	177141410	177141496	E072	28354
chr1	177141587	177141669	E072	28531
chr1	177141817	177141886	E072	28761
chr1	177142156	177142232	E072	29100
chr1	177142487	177142602	E072	29431
chr1	177150351	177150449	E072	37295
chr1	177150590	177151420	E072	37534
chr1	177131509	177131626	E073	18453
chr1	177132857	177132907	E073	19801
chr1	177132999	177134316	E073	19943
chr1	177139645	177139788	E073	26589
chr1	177139847	177140904	E073	26791
chr1	177141013	177141128	E073	27957
chr1	177141265	177141352	E073	28209
chr1	177141410	177141496	E073	28354
chr1	177141587	177141669	E073	28531
chr1	177141817	177141886	E073	28761
chr1	177142156	177142232	E073	29100
chr1	177142487	177142602	E073	29431
chr1	177150590	177151420	E073	37534
chr1	177132999	177134316	E074	19943
chr1	177139645	177139788	E074	26589
chr1	177139847	177140904	E074	26791
chr1	177141013	177141128	E074	27957
chr1	177141265	177141352	E074	28209
chr1	177141410	177141496	E074	28354
chr1	177141587	177141669	E074	28531
chr1	177150351	177150449	E074	37295
chr1	177150590	177151420	E074	37534
chr1	177132857	177132907	E081	19801
chr1	177132999	177134316	E081	19943
chr1	177139847	177140904	E081	26791
chr1	177141265	177141352	E081	28209
chr1	177141410	177141496	E081	28354
chr1	177141587	177141669	E081	28531
chr1	177141817	177141886	E081	28761
chr1	177142156	177142232	E081	29100
chr1	177131509	177131626	E082	18453
chr1	177132857	177132907	E082	19801
chr1	177132999	177134316	E082	19943
chr1	177139645	177139788	E082	26589
chr1	177139847	177140904	E082	26791
chr1	177141013	177141128	E082	27957
chr1	177141587	177141669	E082	28531
chr1	177141817	177141886	E082	28761
chr1	177142156	177142232	E082	29100
chr1	177142487	177142602	E082	29431
chr1	177150351	177150449	E082	37295
chr1	177150590	177151420	E082	37534