rs1111571

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PRMT7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0206 (6190/29948,GnomAD)
G==0187 (5456/29118,TOPMED)
G==0193 (965/5008,1000G)
G==0281 (1084/3854,ALSPAC)
G==0277 (1027/3708,TWINSUK)

Position: chr16:68329278 (GRCh38.p7) (16q22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 142 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 16	NC_000016.10:g.68329278G>A
GRCh37.p13 chr 16	NC_000016.9:g.68363181G>A

Gene: PRMT7, protein arginine methyltransferase 7(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PRMT7 transcript variant 2	NM_001184824.1:c.	N/A	Intron Variant
PRMT7 transcript variant 3	NM_001290018.1:c.	N/A	Intron Variant
PRMT7 transcript variant 1	NM_019023.2:c.	N/A	Intron Variant
PRMT7 transcript variant X2	XM_011523112.2:c.	N/A	Intron Variant
PRMT7 transcript variant X1	XM_011523113.2:c.	N/A	Intron Variant
PRMT7 transcript variant X3	XM_011523115.2:c.	N/A	Intron Variant
PRMT7 transcript variant X5	XM_011523116.2:c.	N/A	Intron Variant
PRMT7 transcript variant X17	XM_011523121.2:c.	N/A	Intron Variant
PRMT7 transcript variant X20	XM_011523124.2:c.	N/A	Intron Variant
PRMT7 transcript variant X21	XM_011523125.2:c.	N/A	Intron Variant
PRMT7 transcript variant X22	XM_011523126.2:c.	N/A	Intron Variant
PRMT7 transcript variant X33	XM_011523128.2:c.	N/A	Intron Variant
PRMT7 transcript variant X48	XM_011523131.2:c.	N/A	Intron Variant
PRMT7 transcript variant X4	XM_017023290.1:c.	N/A	Intron Variant
PRMT7 transcript variant X6	XM_017023291.1:c.	N/A	Intron Variant
PRMT7 transcript variant X8	XM_017023292.1:c.	N/A	Intron Variant
PRMT7 transcript variant X9	XM_017023293.1:c.	N/A	Intron Variant
PRMT7 transcript variant X10	XM_017023294.1:c.	N/A	Intron Variant
PRMT7 transcript variant X11	XM_017023295.1:c.	N/A	Intron Variant
PRMT7 transcript variant X12	XM_017023296.1:c.	N/A	Intron Variant
PRMT7 transcript variant X14	XM_017023297.1:c.	N/A	Intron Variant
PRMT7 transcript variant X15	XM_017023298.1:c.	N/A	Intron Variant
PRMT7 transcript variant X16	XM_017023299.1:c.	N/A	Intron Variant
PRMT7 transcript variant X18	XM_017023300.1:c.	N/A	Intron Variant
PRMT7 transcript variant X19	XM_017023301.1:c.	N/A	Intron Variant
PRMT7 transcript variant X23	XM_017023302.1:c.	N/A	Intron Variant
PRMT7 transcript variant X24	XM_017023303.1:c.	N/A	Intron Variant
PRMT7 transcript variant X25	XM_017023304.1:c.	N/A	Intron Variant
PRMT7 transcript variant X27	XM_017023305.1:c.	N/A	Intron Variant
PRMT7 transcript variant X28	XM_017023306.1:c.	N/A	Intron Variant
PRMT7 transcript variant X29	XM_017023307.1:c.	N/A	Intron Variant
PRMT7 transcript variant X24	XM_017023308.1:c.	N/A	Intron Variant
PRMT7 transcript variant X31	XM_017023309.1:c.	N/A	Intron Variant
PRMT7 transcript variant X26	XM_017023310.1:c.	N/A	Intron Variant
PRMT7 transcript variant X34	XM_017023311.1:c.	N/A	Intron Variant
PRMT7 transcript variant X40	XM_017023312.1:c.	N/A	Intron Variant
PRMT7 transcript variant X45	XM_017023313.1:c.	N/A	Intron Variant
PRMT7 transcript variant X46	XM_017023314.1:c.	N/A	Intron Variant
PRMT7 transcript variant X47	XM_017023315.1:c.	N/A	Intron Variant
PRMT7 transcript variant X49	XM_017023316.1:c.	N/A	Intron Variant
PRMT7 transcript variant X7	XR_001751915.1:n.	N/A	Intron Variant
PRMT7 transcript variant X13	XR_001751916.1:n.	N/A	Intron Variant
PRMT7 transcript variant X26	XR_001751917.1:n.	N/A	Intron Variant
PRMT7 transcript variant X35	XR_001751918.1:n.	N/A	Intron Variant
PRMT7 transcript variant X37	XR_001751919.1:n.	N/A	Intron Variant
PRMT7 transcript variant X33	XR_001751920.1:n.	N/A	Intron Variant
PRMT7 transcript variant X39	XR_001751921.1:n.	N/A	Intron Variant
PRMT7 transcript variant X39	XR_001751922.1:n.	N/A	Intron Variant
PRMT7 transcript variant X40	XR_001751923.1:n.	N/A	Intron Variant
PRMT7 transcript variant X44	XR_001751924.1:n.	N/A	Intron Variant
PRMT7 transcript variant X44	XR_001751925.1:n.	N/A	Intron Variant
PRMT7 transcript variant X36	XR_243413.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.022	A=0.978
1000Genomes	American	Sub	694	G=0.220	A=0.780
1000Genomes	East Asian	Sub	1008	G=0.153	A=0.847
1000Genomes	Europe	Sub	1006	G=0.317	A=0.683
1000Genomes	Global	Study-wide	5008	G=0.193	A=0.807
1000Genomes	South Asian	Sub	978	G=0.320	A=0.680
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.281	A=0.719
The Genome Aggregation Database	African	Sub	8720	G=0.054	A=0.946
The Genome Aggregation Database	American	Sub	838	G=0.240	A=0.760
The Genome Aggregation Database	East Asian	Sub	1618	G=0.149	A=0.851
The Genome Aggregation Database	Europe	Sub	18470	G=0.280	A=0.719
The Genome Aggregation Database	Global	Study-wide	29948	G=0.206	A=0.793
The Genome Aggregation Database	Other	Sub	302	G=0.300	A=0.700
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.187	A=0.812
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.277	A=0.723

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
28452372	1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function.	Gorski M	Sci Rep

P-Value

SNP ID	p-value	Traits	Study
rs1111571	0.00095	alcohol dependence	21314694

eQTL of rs1111571 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr16:68363181	NFATC3	ENSG00000072736.14	G>A	3.5390e-4	244527	Cerebellum
Chr16:68363181	PRMT7	ENSG00000132600.12	G>A	1.0290e-8	18304	Cerebellum
Chr16:68363181	SMPD3	ENSG00000103056.7	G>A	4.0691e-8	-119410	Cerebellum
Chr16:68363181	NFATC3	ENSG00000072736.14	G>A	6.5417e-4	244527	Nucleus_accumbens_basal_ganglia

meQTL of rs1111571 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 )
chr16	68317247	68317322	E067	-45859
chr16	68317411	68317662	E067	-45519
chr16	68346376	68346508	E067	-16673
chr16	68362014	68363453	E067	0
chr16	68394301	68394409	E067	31120
chr16	68394459	68394790	E067	31278
chr16	68394891	68395181	E067	31710
chr16	68399697	68399834	E067	36516
chr16	68399929	68399983	E067	36748
chr16	68400128	68400486	E067	36947
chr16	68411909	68412254	E067	48728
chr16	68412261	68412342	E067	49080
chr16	68316141	68316181	E068	-47000
chr16	68316417	68316472	E068	-46709
chr16	68316900	68317208	E068	-45973
chr16	68317247	68317322	E068	-45859
chr16	68317411	68317662	E068	-45519
chr16	68320831	68320871	E068	-42310
chr16	68320923	68321004	E068	-42177
chr16	68321081	68321152	E068	-42029
chr16	68321232	68322463	E068	-40718
chr16	68323302	68324108	E068	-39073
chr16	68330225	68330275	E068	-32906
chr16	68330326	68330834	E068	-32347
chr16	68332774	68333519	E068	-29662
chr16	68333622	68334719	E068	-28462
chr16	68343413	68343507	E068	-19674
chr16	68367926	68368253	E068	4745
chr16	68368310	68368475	E068	5129
chr16	68380534	68380646	E068	17353
chr16	68380810	68381339	E068	17629
chr16	68381515	68381565	E068	18334
chr16	68381585	68381707	E068	18404
chr16	68381711	68381793	E068	18530
chr16	68381847	68381999	E068	18666
chr16	68397932	68399628	E068	34751
chr16	68399697	68399834	E068	36516
chr16	68399929	68399983	E068	36748
chr16	68400128	68400486	E068	36947
chr16	68400975	68401789	E068	37794
chr16	68408126	68408642	E068	44945
chr16	68411470	68411896	E068	48289
chr16	68411909	68412254	E068	48728
chr16	68412261	68412342	E068	49080
chr16	68412489	68412982	E068	49308
chr16	68412996	68413127	E068	49815
chr16	68316900	68317208	E069	-45973
chr16	68317247	68317322	E069	-45859
chr16	68317411	68317662	E069	-45519
chr16	68333622	68334719	E069	-28462
chr16	68343413	68343507	E069	-19674
chr16	68346376	68346508	E069	-16673
chr16	68381585	68381707	E069	18404
chr16	68381711	68381793	E069	18530
chr16	68381847	68381999	E069	18666
chr16	68382141	68382191	E069	18960
chr16	68384597	68384687	E069	21416
chr16	68384943	68385034	E069	21762
chr16	68394459	68394790	E069	31278
chr16	68394891	68395181	E069	31710
chr16	68401804	68401899	E070	38623
chr16	68401982	68402038	E070	38801
chr16	68402041	68402258	E070	38860
chr16	68402268	68402444	E070	39087
chr16	68402453	68402836	E070	39272
chr16	68402904	68402956	E070	39723
chr16	68403161	68403240	E070	39980
chr16	68403281	68403421	E070	40100
chr16	68403434	68405335	E070	40253
chr16	68410130	68410423	E070	46949
chr16	68410452	68410526	E070	47271
chr16	68410573	68410637	E070	47392
chr16	68410722	68410794	E070	47541
chr16	68316900	68317208	E071	-45973
chr16	68317247	68317322	E071	-45859
chr16	68320923	68321004	E071	-42177
chr16	68321081	68321152	E071	-42029
chr16	68321232	68322463	E071	-40718
chr16	68343413	68343507	E071	-19674
chr16	68362014	68363453	E071	0
chr16	68389639	68390162	E071	26458
chr16	68394891	68395181	E071	31710
chr16	68396117	68396474	E071	32936
chr16	68396487	68396703	E071	33306
chr16	68396758	68397155	E071	33577
chr16	68399697	68399834	E071	36516
chr16	68399929	68399983	E071	36748
chr16	68400128	68400486	E071	36947
chr16	68403434	68405335	E071	40253
chr16	68411470	68411896	E071	48289
chr16	68411909	68412254	E071	48728
chr16	68412261	68412342	E071	49080
chr16	68412489	68412982	E071	49308
chr16	68343413	68343507	E072	-19674
chr16	68362014	68363453	E072	0
chr16	68394055	68394198	E072	30874
chr16	68394459	68394790	E072	31278
chr16	68394891	68395181	E072	31710
chr16	68397932	68399628	E072	34751
chr16	68408010	68408088	E072	44829
chr16	68408126	68408642	E072	44945
chr16	68408660	68408849	E072	45479
chr16	68408905	68409111	E072	45724
chr16	68409286	68409526	E072	46105
chr16	68409601	68409734	E072	46420
chr16	68411909	68412254	E072	48728
chr16	68412261	68412342	E072	49080
chr16	68317411	68317662	E073	-45519
chr16	68324226	68324333	E073	-38848
chr16	68340813	68340919	E073	-22262
chr16	68343413	68343507	E073	-19674
chr16	68369445	68369520	E073	6264
chr16	68394459	68394790	E073	31278
chr16	68397179	68397235	E073	33998
chr16	68397304	68397404	E073	34123
chr16	68397709	68397783	E073	34528
chr16	68397932	68399628	E073	34751
chr16	68399697	68399834	E073	36516
chr16	68399929	68399983	E073	36748
chr16	68400128	68400486	E073	36947
chr16	68403281	68403421	E073	40100
chr16	68403434	68405335	E073	40253
chr16	68408905	68409111	E073	45724
chr16	68409286	68409526	E073	46105
chr16	68409601	68409734	E073	46420
chr16	68411470	68411896	E073	48289
chr16	68411909	68412254	E073	48728
chr16	68412261	68412342	E073	49080
chr16	68412489	68412982	E073	49308
chr16	68316900	68317208	E074	-45973
chr16	68317247	68317322	E074	-45859
chr16	68317411	68317662	E074	-45519
chr16	68343413	68343507	E074	-19674
chr16	68346376	68346508	E074	-16673
chr16	68394459	68394790	E074	31278
chr16	68394891	68395181	E074	31710
chr16	68343413	68343507	E081	-19674
chr16	68346376	68346508	E081	-16673
chr16	68403281	68403421	E081	40100
chr16	68403434	68405335	E081	40253
chr16	68401804	68401899	E082	38623
chr16	68403281	68403421	E082	40100

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr16	68343840	68345778	E067	-17403
chr16	68343840	68345778	E068	-17403
chr16	68343840	68345778	E069	-17403
chr16	68343840	68345778	E070	-17403
chr16	68343840	68345778	E071	-17403
chr16	68343840	68345778	E072	-17403
chr16	68343840	68345778	E073	-17403
chr16	68343840	68345778	E074	-17403
chr16	68343840	68345778	E081	-17403
chr16	68343840	68345778	E082	-17403