rs11038720

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

PHF21A : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0481 (14401/29920,GnomAD)
T=0480 (14000/29118,TOPMED)
T=0426 (2133/5008,1000G)
A==0357 (1376/3854,ALSPAC)
A==0326 (1208/3708,TWINSUK)

Position: chr11:45947110 (GRCh38.p7) (11p11.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 355 Enhancers around

Promoter: 30 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.45947110A>T
GRCh37.p13 chr 11	NC_000011.9:g.45968661A>T

Gene: PHF21A, PHD finger protein 21A(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PHF21A transcript variant 1	NM_001101802.1:c.	N/A	Intron Variant
PHF21A transcript variant 2	NM_016621.3:c.	N/A	Intron Variant
PHF21A transcript variant X21	XM_005252965.4:c.	N/A	Intron Variant
PHF21A transcript variant X8	XM_011520157.2:c.	N/A	Intron Variant
PHF21A transcript variant X1	XM_011520158.2:c.	N/A	Intron Variant
PHF21A transcript variant X2	XM_011520160.2:c.	N/A	Intron Variant
PHF21A transcript variant X3	XM_011520161.2:c.	N/A	Intron Variant
PHF21A transcript variant X4	XM_011520162.2:c.	N/A	Intron Variant
PHF21A transcript variant X7	XM_011520164.2:c.	N/A	Intron Variant
PHF21A transcript variant X9	XM_011520165.2:c.	N/A	Intron Variant
PHF21A transcript variant X6	XM_011520166.2:c.	N/A	Intron Variant
PHF21A transcript variant X10	XM_011520167.2:c.	N/A	Intron Variant
PHF21A transcript variant X11	XM_011520168.2:c.	N/A	Intron Variant
PHF21A transcript variant X13	XM_011520169.2:c.	N/A	Intron Variant
PHF21A transcript variant X18	XM_011520173.2:c.	N/A	Intron Variant
PHF21A transcript variant X17	XM_011520174.2:c.	N/A	Intron Variant
PHF21A transcript variant X24	XM_011520175.2:c.	N/A	Intron Variant
PHF21A transcript variant X33	XM_011520179.2:c.	N/A	Intron Variant
PHF21A transcript variant X5	XM_017017885.1:c.	N/A	Intron Variant
PHF21A transcript variant X12	XM_017017886.1:c.	N/A	Intron Variant
PHF21A transcript variant X14	XM_017017887.1:c.	N/A	Intron Variant
PHF21A transcript variant X14	XM_017017888.1:c.	N/A	Intron Variant
PHF21A transcript variant X15	XM_017017889.1:c.	N/A	Intron Variant
PHF21A transcript variant X16	XM_017017890.1:c.	N/A	Intron Variant
PHF21A transcript variant X22	XM_017017891.1:c.	N/A	Intron Variant
PHF21A transcript variant X23	XM_017017892.1:c.	N/A	Intron Variant
PHF21A transcript variant X25	XM_017017893.1:c.	N/A	Intron Variant
PHF21A transcript variant X26	XM_017017894.1:c.	N/A	Intron Variant
PHF21A transcript variant X27	XM_017017895.1:c.	N/A	Intron Variant
PHF21A transcript variant X28	XM_017017896.1:c.	N/A	Intron Variant
PHF21A transcript variant X29	XM_017017897.1:c.	N/A	Intron Variant
PHF21A transcript variant X29	XM_017017898.1:c.	N/A	Intron Variant
PHF21A transcript variant X31	XM_017017899.1:c.	N/A	Intron Variant
PHF21A transcript variant X32	XM_017017900.1:c.	N/A	Intron Variant
PHF21A transcript variant X33	XM_017017901.1:c.	N/A	Intron Variant
PHF21A transcript variant X36	XM_017017902.1:c.	N/A	Intron Variant
PHF21A transcript variant X35	XM_017017903.1:c.	N/A	Intron Variant
PHF21A transcript variant X37	XM_017017904.1:c.	N/A	Intron Variant
PHF21A transcript variant X39	XM_017017905.1:c.	N/A	Intron Variant
PHF21A transcript variant X39	XM_017017906.1:c.	N/A	Intron Variant
PHF21A transcript variant X41	XM_017017907.1:c.	N/A	Intron Variant
PHF21A transcript variant X42	XM_017017908.1:c.	N/A	Intron Variant
PHF21A transcript variant X38	XR_001747900.1:n.	N/A	Intron Variant
PHF21A transcript variant X41	XR_001747901.1:n.	N/A	Intron Variant
PHF21A transcript variant X43	XR_001747902.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.745	T=0.255
1000Genomes	American	Sub	694	A=0.460	T=0.540
1000Genomes	East Asian	Sub	1008	A=0.771	T=0.229
1000Genomes	Europe	Sub	1006	A=0.348	T=0.652
1000Genomes	Global	Study-wide	5008	A=0.574	T=0.426
1000Genomes	South Asian	Sub	978	A=0.450	T=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.357	T=0.643
The Genome Aggregation Database	African	Sub	8706	A=0.714	T=0.286
The Genome Aggregation Database	American	Sub	838	A=0.510	T=0.490
The Genome Aggregation Database	East Asian	Sub	1616	A=0.795	T=0.205
The Genome Aggregation Database	Europe	Sub	18458	A=0.346	T=0.653
The Genome Aggregation Database	Global	Study-wide	29920	A=0.481	T=0.518
The Genome Aggregation Database	Other	Sub	302	A=0.260	T=0.740
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.519	T=0.480
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.326	T=0.674

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
rs11038720	0.000369	alcohol dependence	21314694

eQTL of rs11038720 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 rs11038720 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 )
chr11	45918746	45918885	E067	-49776
chr11	45918902	45918975	E067	-49686
chr11	45918995	45919089	E067	-49572
chr11	45919188	45919249	E067	-49412
chr11	45919276	45919424	E067	-49237
chr11	45919478	45919528	E067	-49133
chr11	45919589	45919778	E067	-48883
chr11	45919967	45920018	E067	-48643
chr11	45920052	45920237	E067	-48424
chr11	45920352	45920392	E067	-48269
chr11	45924606	45924656	E067	-44005
chr11	45924733	45924863	E067	-43798
chr11	45924902	45924952	E067	-43709
chr11	45925062	45925166	E067	-43495
chr11	45925177	45925227	E067	-43434
chr11	45925275	45925325	E067	-43336
chr11	45928461	45929606	E067	-39055
chr11	45929608	45930112	E067	-38549
chr11	45930149	45930471	E067	-38190
chr11	45930481	45930542	E067	-38119
chr11	45930571	45930690	E067	-37971
chr11	45937854	45937911	E067	-30750
chr11	45937971	45938078	E067	-30583
chr11	45970540	45970590	E067	1879
chr11	45971396	45971436	E067	2735
chr11	45971635	45971930	E067	2974
chr11	45971966	45972016	E067	3305
chr11	46003787	46003912	E067	35126
chr11	46004223	46004309	E067	35562
chr11	46004414	46005566	E067	35753
chr11	46014432	46014510	E067	45771
chr11	46014541	46014786	E067	45880
chr11	46014829	46015872	E067	46168
chr11	46015905	46016425	E067	47244
chr11	46016513	46016703	E067	47852
chr11	45924071	45924285	E068	-44376
chr11	45924407	45924561	E068	-44100
chr11	45924606	45924656	E068	-44005
chr11	45924733	45924863	E068	-43798
chr11	45924902	45924952	E068	-43709
chr11	45925062	45925166	E068	-43495
chr11	45925177	45925227	E068	-43434
chr11	45929608	45930112	E068	-38549
chr11	45930149	45930471	E068	-38190
chr11	45930481	45930542	E068	-38119
chr11	45930571	45930690	E068	-37971
chr11	45930702	45930888	E068	-37773
chr11	45930977	45931047	E068	-37614
chr11	45931181	45931235	E068	-37426
chr11	45931261	45931374	E068	-37287
chr11	45931476	45931576	E068	-37085
chr11	45931711	45931765	E068	-36896
chr11	45937854	45937911	E068	-30750
chr11	45937971	45938078	E068	-30583
chr11	45938135	45938250	E068	-30411
chr11	45941465	45942319	E068	-26342
chr11	45942464	45942542	E068	-26119
chr11	45942593	45942713	E068	-25948
chr11	45942725	45942775	E068	-25886
chr11	45970540	45970590	E068	1879
chr11	45971396	45971436	E068	2735
chr11	45971635	45971930	E068	2974
chr11	45971966	45972016	E068	3305
chr11	45986129	45986300	E068	17468
chr11	45986379	45986988	E068	17718
chr11	46004223	46004309	E068	35562
chr11	46004414	46005566	E068	35753
chr11	46005695	46005749	E068	37034
chr11	46014829	46015872	E068	46168
chr11	46015905	46016425	E068	47244
chr11	46016513	46016703	E068	47852
chr11	45918746	45918885	E069	-49776
chr11	45918902	45918975	E069	-49686
chr11	45918995	45919089	E069	-49572
chr11	45919188	45919249	E069	-49412
chr11	45919276	45919424	E069	-49237
chr11	45924407	45924561	E069	-44100
chr11	45924606	45924656	E069	-44005
chr11	45924733	45924863	E069	-43798
chr11	45924902	45924952	E069	-43709
chr11	45925062	45925166	E069	-43495
chr11	45925177	45925227	E069	-43434
chr11	45925275	45925325	E069	-43336
chr11	45925414	45925554	E069	-43107
chr11	45925771	45925849	E069	-42812
chr11	45925876	45926428	E069	-42233
chr11	45926532	45926582	E069	-42079
chr11	45926772	45926826	E069	-41835
chr11	45926861	45927022	E069	-41639
chr11	45928461	45929606	E069	-39055
chr11	45929608	45930112	E069	-38549
chr11	45930149	45930471	E069	-38190
chr11	45930481	45930542	E069	-38119
chr11	45930571	45930690	E069	-37971
chr11	45937199	45937823	E069	-30838
chr11	45937854	45937911	E069	-30750
chr11	45937971	45938078	E069	-30583
chr11	45938135	45938250	E069	-30411
chr11	45951237	45952405	E069	-16256
chr11	45970540	45970590	E069	1879
chr11	45971396	45971436	E069	2735
chr11	45971635	45971930	E069	2974
chr11	45971966	45972016	E069	3305
chr11	46004414	46005566	E069	35753
chr11	46014829	46015872	E069	46168
chr11	46015905	46016425	E069	47244
chr11	46016513	46016703	E069	47852
chr11	45918746	45918885	E070	-49776
chr11	45918902	45918975	E070	-49686
chr11	45918995	45919089	E070	-49572
chr11	45919188	45919249	E070	-49412
chr11	45919276	45919424	E070	-49237
chr11	45919478	45919528	E070	-49133
chr11	45919589	45919778	E070	-48883
chr11	45919967	45920018	E070	-48643
chr11	45920052	45920237	E070	-48424
chr11	45920352	45920392	E070	-48269
chr11	45936367	45936460	E070	-32201
chr11	45936919	45937000	E070	-31661
chr11	45937051	45937184	E070	-31477
chr11	45937199	45937823	E070	-30838
chr11	45937854	45937911	E070	-30750
chr11	45937971	45938078	E070	-30583
chr11	45938135	45938250	E070	-30411
chr11	45951237	45952405	E070	-16256
chr11	45955523	45955571	E070	-13090
chr11	45955651	45955701	E070	-12960
chr11	45955715	45955989	E070	-12672
chr11	46003544	46003630	E070	34883
chr11	46003787	46003912	E070	35126
chr11	46004223	46004309	E070	35562
chr11	46004414	46005566	E070	35753
chr11	46014144	46014223	E070	45483
chr11	46014432	46014510	E070	45771
chr11	46014541	46014786	E070	45880
chr11	46014829	46015872	E070	46168
chr11	46015905	46016425	E070	47244
chr11	46016513	46016703	E070	47852
chr11	46016833	46017379	E070	48172
chr11	46017547	46017611	E070	48886
chr11	46017636	46017686	E070	48975
chr11	45918902	45918975	E071	-49686
chr11	45918995	45919089	E071	-49572
chr11	45919188	45919249	E071	-49412
chr11	45919276	45919424	E071	-49237
chr11	45925876	45926428	E071	-42233
chr11	45926532	45926582	E071	-42079
chr11	45926772	45926826	E071	-41835
chr11	45926861	45927022	E071	-41639
chr11	45927099	45927316	E071	-41345
chr11	45927354	45927428	E071	-41233
chr11	45927601	45928283	E071	-40378
chr11	45928287	45928336	E071	-40325
chr11	45928461	45929606	E071	-39055
chr11	45929608	45930112	E071	-38549
chr11	45930149	45930471	E071	-38190
chr11	45930481	45930542	E071	-38119
chr11	45930571	45930690	E071	-37971
chr11	45930702	45930888	E071	-37773
chr11	45937051	45937184	E071	-31477
chr11	45937199	45937823	E071	-30838
chr11	45937854	45937911	E071	-30750
chr11	45937971	45938078	E071	-30583
chr11	45938135	45938250	E071	-30411
chr11	45970149	45970245	E071	1488
chr11	45970540	45970590	E071	1879
chr11	45971396	45971436	E071	2735
chr11	45971635	45971930	E071	2974
chr11	45971966	45972016	E071	3305
chr11	45972114	45972164	E071	3453
chr11	45972318	45972394	E071	3657
chr11	45986379	45986988	E071	17718
chr11	46003033	46003114	E071	34372
chr11	46003255	46003370	E071	34594
chr11	46003373	46003473	E071	34712
chr11	46003544	46003630	E071	34883
chr11	46003787	46003912	E071	35126
chr11	46004223	46004309	E071	35562
chr11	46004414	46005566	E071	35753
chr11	46014432	46014510	E071	45771
chr11	46014541	46014786	E071	45880
chr11	46014829	46015872	E071	46168
chr11	46015905	46016425	E071	47244
chr11	46016513	46016703	E071	47852
chr11	46016833	46017379	E071	48172
chr11	45918746	45918885	E072	-49776
chr11	45918902	45918975	E072	-49686
chr11	45918995	45919089	E072	-49572
chr11	45924407	45924561	E072	-44100
chr11	45924606	45924656	E072	-44005
chr11	45924733	45924863	E072	-43798
chr11	45924902	45924952	E072	-43709
chr11	45925062	45925166	E072	-43495
chr11	45925177	45925227	E072	-43434
chr11	45925275	45925325	E072	-43336
chr11	45925414	45925554	E072	-43107
chr11	45928461	45929606	E072	-39055
chr11	45929608	45930112	E072	-38549
chr11	45937854	45937911	E072	-30750
chr11	45937971	45938078	E072	-30583
chr11	45938135	45938250	E072	-30411
chr11	45969989	45970118	E072	1328
chr11	45970149	45970245	E072	1488
chr11	45970540	45970590	E072	1879
chr11	45971396	45971436	E072	2735
chr11	45971635	45971930	E072	2974
chr11	45971966	45972016	E072	3305
chr11	45972114	45972164	E072	3453
chr11	46004223	46004309	E072	35562
chr11	46004414	46005566	E072	35753
chr11	46005695	46005749	E072	37034
chr11	46014829	46015872	E072	46168
chr11	45924407	45924561	E073	-44100
chr11	45924606	45924656	E073	-44005
chr11	45924733	45924863	E073	-43798
chr11	45924902	45924952	E073	-43709
chr11	45925062	45925166	E073	-43495
chr11	45925177	45925227	E073	-43434
chr11	45925275	45925325	E073	-43336
chr11	45925414	45925554	E073	-43107
chr11	45925771	45925849	E073	-42812
chr11	45929608	45930112	E073	-38549
chr11	45930149	45930471	E073	-38190
chr11	45937854	45937911	E073	-30750
chr11	45937971	45938078	E073	-30583
chr11	45938135	45938250	E073	-30411
chr11	45951237	45952405	E073	-16256
chr11	45970540	45970590	E073	1879
chr11	46003787	46003912	E073	35126
chr11	46004223	46004309	E073	35562
chr11	46004414	46005566	E073	35753
chr11	46014829	46015872	E073	46168
chr11	46015905	46016425	E073	47244
chr11	46016513	46016703	E073	47852
chr11	45918746	45918885	E074	-49776
chr11	45920052	45920237	E074	-48424
chr11	45920352	45920392	E074	-48269
chr11	45924407	45924561	E074	-44100
chr11	45924606	45924656	E074	-44005
chr11	45924733	45924863	E074	-43798
chr11	45924902	45924952	E074	-43709
chr11	45925062	45925166	E074	-43495
chr11	45925177	45925227	E074	-43434
chr11	45925275	45925325	E074	-43336
chr11	45925414	45925554	E074	-43107
chr11	45925771	45925849	E074	-42812
chr11	45925876	45926428	E074	-42233
chr11	45926532	45926582	E074	-42079
chr11	45926772	45926826	E074	-41835
chr11	45928461	45929606	E074	-39055
chr11	45929608	45930112	E074	-38549
chr11	45930149	45930471	E074	-38190
chr11	45930481	45930542	E074	-38119
chr11	45930571	45930690	E074	-37971
chr11	45930702	45930888	E074	-37773
chr11	45931476	45931576	E074	-37085
chr11	45931711	45931765	E074	-36896
chr11	45931889	45931951	E074	-36710
chr11	45937199	45937823	E074	-30838
chr11	45937854	45937911	E074	-30750
chr11	45937971	45938078	E074	-30583
chr11	45938135	45938250	E074	-30411
chr11	45941465	45942319	E074	-26342
chr11	45942464	45942542	E074	-26119
chr11	45942593	45942713	E074	-25948
chr11	45942725	45942775	E074	-25886
chr11	45970540	45970590	E074	1879
chr11	46004223	46004309	E074	35562
chr11	46004414	46005566	E074	35753
chr11	46005695	46005749	E074	37034
chr11	46005806	46006209	E074	37145
chr11	46014432	46014510	E074	45771
chr11	46014541	46014786	E074	45880
chr11	46014829	46015872	E074	46168
chr11	46015905	46016425	E074	47244
chr11	45920052	45920237	E081	-48424
chr11	45920352	45920392	E081	-48269
chr11	45923097	45923468	E081	-45193
chr11	45923541	45923595	E081	-45066
chr11	45929608	45930112	E081	-38549
chr11	45930149	45930471	E081	-38190
chr11	45937854	45937911	E081	-30750
chr11	45937971	45938078	E081	-30583
chr11	45938135	45938250	E081	-30411
chr11	45951237	45952405	E081	-16256
chr11	45954560	45955495	E081	-13166
chr11	45955523	45955571	E081	-13090
chr11	45955651	45955701	E081	-12960
chr11	45955715	45955989	E081	-12672
chr11	45966689	45966814	E081	-1847
chr11	45966876	45966964	E081	-1697
chr11	45967000	45967441	E081	-1220
chr11	45986379	45986988	E081	17718
chr11	46003787	46003912	E081	35126
chr11	46004223	46004309	E081	35562
chr11	46004414	46005566	E081	35753
chr11	46005695	46005749	E081	37034
chr11	46005806	46006209	E081	37145
chr11	46006324	46006374	E081	37663
chr11	46009363	46009497	E081	40702
chr11	46010333	46010466	E081	41672
chr11	46010573	46010668	E081	41912
chr11	46012152	46012235	E081	43491
chr11	46012299	46012712	E081	43638
chr11	46013585	46013635	E081	44924
chr11	46013661	46013776	E081	45000
chr11	46014144	46014223	E081	45483
chr11	46014432	46014510	E081	45771
chr11	46014541	46014786	E081	45880
chr11	46014829	46015872	E081	46168
chr11	46015905	46016425	E081	47244
chr11	46016513	46016703	E081	47852
chr11	46016833	46017379	E081	48172
chr11	46017547	46017611	E081	48886
chr11	46017636	46017686	E081	48975
chr11	46018221	46018271	E081	49560
chr11	45923541	45923595	E082	-45066
chr11	45923629	45923905	E082	-44756
chr11	45924071	45924285	E082	-44376
chr11	45924407	45924561	E082	-44100
chr11	45936521	45936602	E082	-32059
chr11	45937051	45937184	E082	-31477
chr11	45937199	45937823	E082	-30838
chr11	45937854	45937911	E082	-30750
chr11	45937971	45938078	E082	-30583
chr11	45938135	45938250	E082	-30411
chr11	45946115	45946261	E082	-22400
chr11	45946293	45946441	E082	-22220
chr11	45954560	45955495	E082	-13166
chr11	45955523	45955571	E082	-13090
chr11	45955651	45955701	E082	-12960
chr11	45955715	45955989	E082	-12672
chr11	46003255	46003370	E082	34594
chr11	46003373	46003473	E082	34712
chr11	46003544	46003630	E082	34883
chr11	46003787	46003912	E082	35126
chr11	46004223	46004309	E082	35562
chr11	46005695	46005749	E082	37034
chr11	46005806	46006209	E082	37145
chr11	46006324	46006374	E082	37663
chr11	46009363	46009497	E082	40702
chr11	46009499	46009560	E082	40838
chr11	46012152	46012235	E082	43491
chr11	46012299	46012712	E082	43638
chr11	46013585	46013635	E082	44924
chr11	46013661	46013776	E082	45000
chr11	46014144	46014223	E082	45483
chr11	46014432	46014510	E082	45771
chr11	46014541	46014786	E082	45880
chr11	46014829	46015872	E082	46168
chr11	46015905	46016425	E082	47244
chr11	46016513	46016703	E082	47852
chr11	46016833	46017379	E082	48172
chr11	46017547	46017611	E082	48886
chr11	46017636	46017686	E082	48975

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr11	45920757	45921744	E067	-46917
chr11	45921968	45923088	E067	-45573
chr11	45938532	45941211	E067	-27450
chr11	45920757	45921744	E068	-46917
chr11	45921968	45923088	E068	-45573
chr11	45938532	45941211	E068	-27450
chr11	45942830	45945276	E068	-23385
chr11	45920757	45921744	E069	-46917
chr11	45921968	45923088	E069	-45573
chr11	45938532	45941211	E069	-27450
chr11	45920757	45921744	E070	-46917
chr11	45921968	45923088	E070	-45573
chr11	45938532	45941211	E070	-27450
chr11	45942830	45945276	E070	-23385
chr11	45920757	45921744	E071	-46917
chr11	45921968	45923088	E071	-45573
chr11	45938532	45941211	E071	-27450
chr11	45920757	45921744	E072	-46917
chr11	45921968	45923088	E072	-45573
chr11	45938532	45941211	E072	-27450
chr11	45920757	45921744	E073	-46917
chr11	45921968	45923088	E073	-45573
chr11	45938532	45941211	E073	-27450
chr11	45920757	45921744	E074	-46917
chr11	45921968	45923088	E074	-45573
chr11	45938532	45941211	E074	-27450
chr11	45938532	45941211	E081	-27450
chr11	45920757	45921744	E082	-46917
chr11	45921968	45923088	E082	-45573
chr11	45938532	45941211	E082	-27450