rs4912013

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

IFFO2 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0483 (14460/29930,GnomAD)
T==0499 (14530/29118,TOPMED)
T==0444 (2224/5008,1000G)
C=0428 (1651/3854,ALSPAC)
C=0410 (1521/3708,TWINSUK)

Position: chr1:18958070 (GRCh38.p7) (1p36.13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 387 Enhancers around

Promoter: 17 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.18958070T>C
GRCh37.p13 chr 1	NC_000001.10:g.19284564T>C

Gene: IFFO2, intermediate filament family orphan 2(minus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
IFFO2 transcript	NM_001136265.1:c.	N/A	Upstream Transcript Variant
IFFO2 transcript variant X1	XM_011540630.2:c.	N/A	Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.415	C=0.585
1000Genomes	American	Sub	694	T=0.360	C=0.640
1000Genomes	East Asian	Sub	1008	T=0.260	C=0.740
1000Genomes	Europe	Sub	1006	T=0.604	C=0.396
1000Genomes	Global	Study-wide	5008	T=0.444	C=0.556
1000Genomes	South Asian	Sub	978	T=0.570	C=0.430
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.572	C=0.428
The Genome Aggregation Database	African	Sub	8710	T=0.465	C=0.535
The Genome Aggregation Database	American	Sub	836	T=0.330	C=0.670
The Genome Aggregation Database	East Asian	Sub	1614	T=0.281	C=0.719
The Genome Aggregation Database	Europe	Sub	18470	T=0.570	C=0.430
The Genome Aggregation Database	Global	Study-wide	29930	T=0.516	C=0.483
The Genome Aggregation Database	Other	Sub	300	T=0.570	C=0.430
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.499	C=0.501
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.590	C=0.410

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs4912013	0.000145	alcohol dependence	21314694

eQTL of rs4912013 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 rs4912013 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	19248165	19248231	E067	-36333
chr1	19248260	19248399	E067	-36165
chr1	19248409	19248687	E067	-35877
chr1	19248699	19249245	E067	-35319
chr1	19249279	19249346	E067	-35218
chr1	19249354	19249731	E067	-34833
chr1	19250059	19250142	E067	-34422
chr1	19250146	19250719	E067	-33845
chr1	19250731	19251165	E067	-33399
chr1	19251327	19251423	E067	-33141
chr1	19252754	19254692	E067	-29872
chr1	19254879	19255026	E067	-29538
chr1	19255329	19255400	E067	-29164
chr1	19255537	19255631	E067	-28933
chr1	19255643	19255708	E067	-28856
chr1	19258325	19258403	E067	-26161
chr1	19258926	19259358	E067	-25206
chr1	19259497	19259691	E067	-24873
chr1	19259922	19260012	E067	-24552
chr1	19261215	19261421	E067	-23143
chr1	19261794	19261935	E067	-22629
chr1	19265269	19265525	E067	-19039
chr1	19265564	19265767	E067	-18797
chr1	19265907	19267026	E067	-17538
chr1	19267119	19269270	E067	-15294
chr1	19270410	19270590	E067	-13974
chr1	19271227	19271353	E067	-13211
chr1	19271449	19271489	E067	-13075
chr1	19271540	19271648	E067	-12916
chr1	19271756	19272249	E067	-12315
chr1	19272284	19272634	E067	-11930
chr1	19273442	19273847	E067	-10717
chr1	19273920	19273995	E067	-10569
chr1	19274155	19274405	E067	-10159
chr1	19274455	19274505	E067	-10059
chr1	19274747	19274849	E067	-9715
chr1	19274935	19275407	E067	-9157
chr1	19277880	19279587	E067	-4977
chr1	19279772	19279822	E067	-4742
chr1	19284291	19284462	E067	-102
chr1	19315950	19316196	E067	31386
chr1	19324060	19324311	E067	39496
chr1	19324755	19325129	E067	40191
chr1	19239448	19240189	E068	-44375
chr1	19248165	19248231	E068	-36333
chr1	19248260	19248399	E068	-36165
chr1	19248409	19248687	E068	-35877
chr1	19248699	19249245	E068	-35319
chr1	19249279	19249346	E068	-35218
chr1	19250059	19250142	E068	-34422
chr1	19250146	19250719	E068	-33845
chr1	19250731	19251165	E068	-33399
chr1	19251327	19251423	E068	-33141
chr1	19252754	19254692	E068	-29872
chr1	19254879	19255026	E068	-29538
chr1	19255329	19255400	E068	-29164
chr1	19255537	19255631	E068	-28933
chr1	19255643	19255708	E068	-28856
chr1	19256086	19256126	E068	-28438
chr1	19258325	19258403	E068	-26161
chr1	19258926	19259358	E068	-25206
chr1	19259497	19259691	E068	-24873
chr1	19259922	19260012	E068	-24552
chr1	19261215	19261421	E068	-23143
chr1	19261794	19261935	E068	-22629
chr1	19262603	19262700	E068	-21864
chr1	19263102	19263272	E068	-21292
chr1	19263315	19263478	E068	-21086
chr1	19263595	19264027	E068	-20537
chr1	19264031	19264267	E068	-20297
chr1	19264337	19264448	E068	-20116
chr1	19264931	19265239	E068	-19325
chr1	19265269	19265525	E068	-19039
chr1	19265564	19265767	E068	-18797
chr1	19265907	19267026	E068	-17538
chr1	19267119	19269270	E068	-15294
chr1	19270410	19270590	E068	-13974
chr1	19271227	19271353	E068	-13211
chr1	19271449	19271489	E068	-13075
chr1	19271540	19271648	E068	-12916
chr1	19271756	19272249	E068	-12315
chr1	19272284	19272634	E068	-11930
chr1	19272797	19272837	E068	-11727
chr1	19272842	19272898	E068	-11666
chr1	19273442	19273847	E068	-10717
chr1	19273920	19273995	E068	-10569
chr1	19274155	19274405	E068	-10159
chr1	19274455	19274505	E068	-10059
chr1	19274747	19274849	E068	-9715
chr1	19274935	19275407	E068	-9157
chr1	19277880	19279587	E068	-4977
chr1	19284291	19284462	E068	-102
chr1	19289009	19289149	E068	4445
chr1	19323341	19323523	E068	38777
chr1	19323542	19323592	E068	38978
chr1	19324060	19324311	E068	39496
chr1	19324755	19325129	E068	40191
chr1	19234919	19235012	E069	-49552
chr1	19235033	19235166	E069	-49398
chr1	19239448	19240189	E069	-44375
chr1	19248165	19248231	E069	-36333
chr1	19248260	19248399	E069	-36165
chr1	19248409	19248687	E069	-35877
chr1	19249354	19249731	E069	-34833
chr1	19250059	19250142	E069	-34422
chr1	19250146	19250719	E069	-33845
chr1	19250731	19251165	E069	-33399
chr1	19251327	19251423	E069	-33141
chr1	19251484	19251524	E069	-33040
chr1	19251613	19251663	E069	-32901
chr1	19251923	19251973	E069	-32591
chr1	19251996	19252109	E069	-32455
chr1	19252754	19254692	E069	-29872
chr1	19254879	19255026	E069	-29538
chr1	19255329	19255400	E069	-29164
chr1	19255537	19255631	E069	-28933
chr1	19258325	19258403	E069	-26161
chr1	19258926	19259358	E069	-25206
chr1	19259497	19259691	E069	-24873
chr1	19259922	19260012	E069	-24552
chr1	19261215	19261421	E069	-23143
chr1	19261794	19261935	E069	-22629
chr1	19264337	19264448	E069	-20116
chr1	19264931	19265239	E069	-19325
chr1	19265564	19265767	E069	-18797
chr1	19265907	19267026	E069	-17538
chr1	19267119	19269270	E069	-15294
chr1	19270410	19270590	E069	-13974
chr1	19271227	19271353	E069	-13211
chr1	19271449	19271489	E069	-13075
chr1	19271540	19271648	E069	-12916
chr1	19271756	19272249	E069	-12315
chr1	19272284	19272634	E069	-11930
chr1	19272797	19272837	E069	-11727
chr1	19272842	19272898	E069	-11666
chr1	19273442	19273847	E069	-10717
chr1	19273920	19273995	E069	-10569
chr1	19274155	19274405	E069	-10159
chr1	19274455	19274505	E069	-10059
chr1	19274747	19274849	E069	-9715
chr1	19274935	19275407	E069	-9157
chr1	19277880	19279587	E069	-4977
chr1	19284291	19284462	E069	-102
chr1	19315950	19316196	E069	31386
chr1	19316513	19316759	E069	31949
chr1	19323341	19323523	E069	38777
chr1	19323542	19323592	E069	38978
chr1	19324060	19324311	E069	39496
chr1	19324755	19325129	E069	40191
chr1	19325787	19326226	E069	41223
chr1	19234919	19235012	E070	-49552
chr1	19248409	19248687	E070	-35877
chr1	19248699	19249245	E070	-35319
chr1	19249279	19249346	E070	-35218
chr1	19249354	19249731	E070	-34833
chr1	19271449	19271489	E070	-13075
chr1	19271540	19271648	E070	-12916
chr1	19271756	19272249	E070	-12315
chr1	19272284	19272634	E070	-11930
chr1	19234919	19235012	E071	-49552
chr1	19235033	19235166	E071	-49398
chr1	19239448	19240189	E071	-44375
chr1	19240755	19240863	E071	-43701
chr1	19240933	19240983	E071	-43581
chr1	19248165	19248231	E071	-36333
chr1	19248260	19248399	E071	-36165
chr1	19250059	19250142	E071	-34422
chr1	19250146	19250719	E071	-33845
chr1	19250731	19251165	E071	-33399
chr1	19251327	19251423	E071	-33141
chr1	19251484	19251524	E071	-33040
chr1	19251613	19251663	E071	-32901
chr1	19252754	19254692	E071	-29872
chr1	19254879	19255026	E071	-29538
chr1	19255329	19255400	E071	-29164
chr1	19255537	19255631	E071	-28933
chr1	19258926	19259358	E071	-25206
chr1	19259497	19259691	E071	-24873
chr1	19263102	19263272	E071	-21292
chr1	19263315	19263478	E071	-21086
chr1	19264337	19264448	E071	-20116
chr1	19265269	19265525	E071	-19039
chr1	19265564	19265767	E071	-18797
chr1	19265907	19267026	E071	-17538
chr1	19267119	19269270	E071	-15294
chr1	19270410	19270590	E071	-13974
chr1	19271449	19271489	E071	-13075
chr1	19271540	19271648	E071	-12916
chr1	19271756	19272249	E071	-12315
chr1	19272284	19272634	E071	-11930
chr1	19272797	19272837	E071	-11727
chr1	19272842	19272898	E071	-11666
chr1	19273442	19273847	E071	-10717
chr1	19273920	19273995	E071	-10569
chr1	19274155	19274405	E071	-10159
chr1	19274455	19274505	E071	-10059
chr1	19274747	19274849	E071	-9715
chr1	19274935	19275407	E071	-9157
chr1	19277880	19279587	E071	-4977
chr1	19284291	19284462	E071	-102
chr1	19315950	19316196	E071	31386
chr1	19323341	19323523	E071	38777
chr1	19323542	19323592	E071	38978
chr1	19324060	19324311	E071	39496
chr1	19324755	19325129	E071	40191
chr1	19325787	19326226	E071	41223
chr1	19239448	19240189	E072	-44375
chr1	19248165	19248231	E072	-36333
chr1	19248260	19248399	E072	-36165
chr1	19248409	19248687	E072	-35877
chr1	19248699	19249245	E072	-35319
chr1	19249279	19249346	E072	-35218
chr1	19249354	19249731	E072	-34833
chr1	19250059	19250142	E072	-34422
chr1	19250731	19251165	E072	-33399
chr1	19251327	19251423	E072	-33141
chr1	19251484	19251524	E072	-33040
chr1	19251613	19251663	E072	-32901
chr1	19251923	19251973	E072	-32591
chr1	19251996	19252109	E072	-32455
chr1	19252754	19254692	E072	-29872
chr1	19254879	19255026	E072	-29538
chr1	19255329	19255400	E072	-29164
chr1	19255537	19255631	E072	-28933
chr1	19258325	19258403	E072	-26161
chr1	19258926	19259358	E072	-25206
chr1	19259497	19259691	E072	-24873
chr1	19259922	19260012	E072	-24552
chr1	19261794	19261935	E072	-22629
chr1	19262015	19262185	E072	-22379
chr1	19262603	19262700	E072	-21864
chr1	19263102	19263272	E072	-21292
chr1	19263315	19263478	E072	-21086
chr1	19263595	19264027	E072	-20537
chr1	19264031	19264267	E072	-20297
chr1	19264337	19264448	E072	-20116
chr1	19264931	19265239	E072	-19325
chr1	19265269	19265525	E072	-19039
chr1	19265564	19265767	E072	-18797
chr1	19265907	19267026	E072	-17538
chr1	19267119	19269270	E072	-15294
chr1	19270410	19270590	E072	-13974
chr1	19271756	19272249	E072	-12315
chr1	19272284	19272634	E072	-11930
chr1	19272797	19272837	E072	-11727
chr1	19272842	19272898	E072	-11666
chr1	19273442	19273847	E072	-10717
chr1	19273920	19273995	E072	-10569
chr1	19274155	19274405	E072	-10159
chr1	19274455	19274505	E072	-10059
chr1	19274747	19274849	E072	-9715
chr1	19284291	19284462	E072	-102
chr1	19284627	19284738	E072	63
chr1	19284763	19284927	E072	199
chr1	19315950	19316196	E072	31386
chr1	19323341	19323523	E072	38777
chr1	19323542	19323592	E072	38978
chr1	19324060	19324311	E072	39496
chr1	19324755	19325129	E072	40191
chr1	19325787	19326226	E072	41223
chr1	19234919	19235012	E073	-49552
chr1	19235033	19235166	E073	-49398
chr1	19235202	19235252	E073	-49312
chr1	19235345	19235407	E073	-49157
chr1	19239448	19240189	E073	-44375
chr1	19248165	19248231	E073	-36333
chr1	19248260	19248399	E073	-36165
chr1	19248409	19248687	E073	-35877
chr1	19248699	19249245	E073	-35319
chr1	19249279	19249346	E073	-35218
chr1	19249354	19249731	E073	-34833
chr1	19250059	19250142	E073	-34422
chr1	19250146	19250719	E073	-33845
chr1	19250731	19251165	E073	-33399
chr1	19251327	19251423	E073	-33141
chr1	19251484	19251524	E073	-33040
chr1	19251613	19251663	E073	-32901
chr1	19251923	19251973	E073	-32591
chr1	19251996	19252109	E073	-32455
chr1	19252190	19252256	E073	-32308
chr1	19252754	19254692	E073	-29872
chr1	19254879	19255026	E073	-29538
chr1	19255329	19255400	E073	-29164
chr1	19255537	19255631	E073	-28933
chr1	19255643	19255708	E073	-28856
chr1	19256086	19256126	E073	-28438
chr1	19257296	19257336	E073	-27228
chr1	19258325	19258403	E073	-26161
chr1	19258926	19259358	E073	-25206
chr1	19259497	19259691	E073	-24873
chr1	19259922	19260012	E073	-24552
chr1	19263595	19264027	E073	-20537
chr1	19264031	19264267	E073	-20297
chr1	19264337	19264448	E073	-20116
chr1	19264931	19265239	E073	-19325
chr1	19265269	19265525	E073	-19039
chr1	19265564	19265767	E073	-18797
chr1	19265907	19267026	E073	-17538
chr1	19267119	19269270	E073	-15294
chr1	19270410	19270590	E073	-13974
chr1	19271756	19272249	E073	-12315
chr1	19272284	19272634	E073	-11930
chr1	19272797	19272837	E073	-11727
chr1	19272842	19272898	E073	-11666
chr1	19273442	19273847	E073	-10717
chr1	19273920	19273995	E073	-10569
chr1	19274155	19274405	E073	-10159
chr1	19274455	19274505	E073	-10059
chr1	19274747	19274849	E073	-9715
chr1	19277880	19279587	E073	-4977
chr1	19279772	19279822	E073	-4742
chr1	19284291	19284462	E073	-102
chr1	19323341	19323523	E073	38777
chr1	19323542	19323592	E073	38978
chr1	19324060	19324311	E073	39496
chr1	19324755	19325129	E073	40191
chr1	19239448	19240189	E074	-44375
chr1	19248165	19248231	E074	-36333
chr1	19248260	19248399	E074	-36165
chr1	19248409	19248687	E074	-35877
chr1	19250059	19250142	E074	-34422
chr1	19250146	19250719	E074	-33845
chr1	19250731	19251165	E074	-33399
chr1	19251327	19251423	E074	-33141
chr1	19252754	19254692	E074	-29872
chr1	19254879	19255026	E074	-29538
chr1	19255329	19255400	E074	-29164
chr1	19255537	19255631	E074	-28933
chr1	19255643	19255708	E074	-28856
chr1	19258325	19258403	E074	-26161
chr1	19258926	19259358	E074	-25206
chr1	19259497	19259691	E074	-24873
chr1	19259922	19260012	E074	-24552
chr1	19261215	19261421	E074	-23143
chr1	19261794	19261935	E074	-22629
chr1	19262015	19262185	E074	-22379
chr1	19262603	19262700	E074	-21864
chr1	19263102	19263272	E074	-21292
chr1	19263315	19263478	E074	-21086
chr1	19263595	19264027	E074	-20537
chr1	19264031	19264267	E074	-20297
chr1	19264337	19264448	E074	-20116
chr1	19264931	19265239	E074	-19325
chr1	19265269	19265525	E074	-19039
chr1	19265564	19265767	E074	-18797
chr1	19265907	19267026	E074	-17538
chr1	19270410	19270590	E074	-13974
chr1	19271227	19271353	E074	-13211
chr1	19271449	19271489	E074	-13075
chr1	19271540	19271648	E074	-12916
chr1	19271756	19272249	E074	-12315
chr1	19272284	19272634	E074	-11930
chr1	19272797	19272837	E074	-11727
chr1	19272842	19272898	E074	-11666
chr1	19273442	19273847	E074	-10717
chr1	19273920	19273995	E074	-10569
chr1	19274155	19274405	E074	-10159
chr1	19274455	19274505	E074	-10059
chr1	19274747	19274849	E074	-9715
chr1	19274935	19275407	E074	-9157
chr1	19277880	19279587	E074	-4977
chr1	19284291	19284462	E074	-102
chr1	19284627	19284738	E074	63
chr1	19284763	19284927	E074	199
chr1	19315950	19316196	E074	31386
chr1	19323341	19323523	E074	38777
chr1	19323542	19323592	E074	38978
chr1	19324060	19324311	E074	39496
chr1	19324755	19325129	E074	40191
chr1	19248165	19248231	E081	-36333
chr1	19248260	19248399	E081	-36165
chr1	19248409	19248687	E081	-35877
chr1	19248699	19249245	E081	-35319
chr1	19249279	19249346	E081	-35218
chr1	19249354	19249731	E081	-34833
chr1	19264931	19265239	E081	-19325
chr1	19265269	19265525	E081	-19039
chr1	19271227	19271353	E081	-13211
chr1	19271449	19271489	E081	-13075
chr1	19271540	19271648	E081	-12916
chr1	19271756	19272249	E081	-12315
chr1	19272284	19272634	E081	-11930
chr1	19254879	19255026	E082	-29538
chr1	19265269	19265525	E082	-19039
chr1	19265564	19265767	E082	-18797
chr1	19271756	19272249	E082	-12315
chr1	19272284	19272634	E082	-11930

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	19281628	19282711	E067	-1853
chr1	19282759	19284254	E067	-310
chr1	19281628	19282711	E068	-1853
chr1	19282759	19284254	E068	-310
chr1	19281628	19282711	E069	-1853
chr1	19282759	19284254	E069	-310
chr1	19282759	19284254	E070	-310
chr1	19281628	19282711	E071	-1853
chr1	19282759	19284254	E071	-310
chr1	19281628	19282711	E072	-1853
chr1	19282759	19284254	E072	-310
chr1	19281628	19282711	E073	-1853
chr1	19282759	19284254	E073	-310
chr1	19281628	19282711	E074	-1853
chr1	19282759	19284254	E074	-310
chr1	19281628	19282711	E082	-1853
chr1	19282759	19284254	E082	-310