rs701837

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

PDZD7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0354 (10509/29626,GnomAD)
T==0341 (9935/29118,TOPMED)
T==0473 (2368/5008,1000G)
T==0331 (1277/3854,ALSPAC)
T==0328 (1218/3708,TWINSUK)

Position: chr10:101015448 (GRCh38.p7) (10q24.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 295 Enhancers around

Promoter: 33 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 10	NC_000010.11:g.101015448T>C
GRCh37.p13 chr 10	NC_000010.10:g.102775205T>C
PDZD7 RefSeqGene	NG_028030.1:g.20710A>G

Gene: PDZD7, PDZ domain containing 7(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PDZD7 transcript variant 1	NM_001195263.1:c.	N/A	Intron Variant
PDZD7 transcript variant 2	NM_024895.4:c.	N/A	Genic Downstream Transcript Variant
PDZD7 transcript variant X6	XM_005270165.2:c.	N/A	Intron Variant
PDZD7 transcript variant X1	XM_011540177.2:c.	N/A	Intron Variant
PDZD7 transcript variant X2	XM_011540178.2:c.	N/A	Intron Variant
PDZD7 transcript variant X3	XM_011540179.2:c.	N/A	Intron Variant
PDZD7 transcript variant X7	XM_011540181.2:c.	N/A	Intron Variant
PDZD7 transcript variant X8	XM_011540182.2:c.	N/A	Genic Downstream Transcript Variant
PDZD7 transcript variant X9	XM_011540183.2:c.	N/A	Genic Downstream Transcript Variant
PDZD7 transcript variant X4	XM_017016667.1:c.	N/A	Genic Downstream Transcript Variant
PDZD7 transcript variant X10	XM_017016668.1:c.	N/A	Genic Downstream Transcript Variant
PDZD7 transcript variant X11	XR_945816.2:n.	N/A	Intron Variant
PDZD7 transcript variant X5	XR_001747203.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.305	C=0.695
1000Genomes	American	Sub	694	T=0.400	C=0.600
1000Genomes	East Asian	Sub	1008	T=0.759	C=0.241
1000Genomes	Europe	Sub	1006	T=0.351	C=0.649
1000Genomes	Global	Study-wide	5008	T=0.473	C=0.527
1000Genomes	South Asian	Sub	978	T=0.580	C=0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.331	C=0.669
The Genome Aggregation Database	African	Sub	8602	T=0.304	C=0.696
The Genome Aggregation Database	American	Sub	832	T=0.420	C=0.580
The Genome Aggregation Database	East Asian	Sub	1552	T=0.755	C=0.245
The Genome Aggregation Database	Europe	Sub	18338	T=0.341	C=0.658
The Genome Aggregation Database	Global	Study-wide	29626	T=0.354	C=0.645
The Genome Aggregation Database	Other	Sub	302	T=0.330	C=0.670
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.341	C=0.658
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.328	C=0.672

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs701837	0.00000119	alcoholism	pha002892
rs701837	0.0000012	alcohol dependence	20201924

eQTL of rs701837 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 rs701837 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 )
chr10	102728355	102728532	E067	-46673
chr10	102745742	102745889	E067	-29316
chr10	102753817	102754682	E067	-20523
chr10	102762046	102762160	E067	-13045
chr10	102762161	102762224	E067	-12981
chr10	102762273	102762339	E067	-12866
chr10	102762356	102762452	E067	-12753
chr10	102762787	102762894	E067	-12311
chr10	102765153	102765430	E067	-9775
chr10	102765435	102765510	E067	-9695
chr10	102765673	102765723	E067	-9482
chr10	102766095	102766175	E067	-9030
chr10	102766265	102767583	E067	-7622
chr10	102767623	102767754	E067	-7451
chr10	102767799	102767968	E067	-7237
chr10	102768005	102768369	E067	-6836
chr10	102768489	102768915	E067	-6290
chr10	102769055	102769113	E067	-6092
chr10	102769124	102769222	E067	-5983
chr10	102771918	102772010	E067	-3195
chr10	102772016	102772109	E067	-3096
chr10	102772207	102772352	E067	-2853
chr10	102772357	102773586	E067	-1619
chr10	102773844	102774588	E067	-617
chr10	102799745	102800261	E067	24540
chr10	102728355	102728532	E068	-46673
chr10	102744951	102745050	E068	-30155
chr10	102745289	102745352	E068	-29853
chr10	102745362	102745445	E068	-29760
chr10	102745742	102745889	E068	-29316
chr10	102753817	102754682	E068	-20523
chr10	102754806	102754934	E068	-20271
chr10	102755016	102755376	E068	-19829
chr10	102755404	102755529	E068	-19676
chr10	102755570	102755713	E068	-19492
chr10	102755746	102755829	E068	-19376
chr10	102755847	102755898	E068	-19307
chr10	102762046	102762160	E068	-13045
chr10	102762161	102762224	E068	-12981
chr10	102762273	102762339	E068	-12866
chr10	102762356	102762452	E068	-12753
chr10	102762787	102762894	E068	-12311
chr10	102763203	102763315	E068	-11890
chr10	102763320	102763381	E068	-11824
chr10	102763389	102763440	E068	-11765
chr10	102763831	102763900	E068	-11305
chr10	102766265	102767583	E068	-7622
chr10	102767623	102767754	E068	-7451
chr10	102767799	102767968	E068	-7237
chr10	102768005	102768369	E068	-6836
chr10	102768489	102768915	E068	-6290
chr10	102769055	102769113	E068	-6092
chr10	102769124	102769222	E068	-5983
chr10	102771193	102771861	E068	-3344
chr10	102771918	102772010	E068	-3195
chr10	102772016	102772109	E068	-3096
chr10	102772207	102772352	E068	-2853
chr10	102772357	102773586	E068	-1619
chr10	102773844	102774588	E068	-617
chr10	102774628	102775581	E068	0
chr10	102799585	102799668	E068	24380
chr10	102799745	102800261	E068	24540
chr10	102800626	102800764	E068	25421
chr10	102727954	102728353	E069	-46852
chr10	102728355	102728532	E069	-46673
chr10	102745742	102745889	E069	-29316
chr10	102748481	102748633	E069	-26572
chr10	102748722	102748895	E069	-26310
chr10	102748929	102748995	E069	-26210
chr10	102749023	102749150	E069	-26055
chr10	102749153	102749228	E069	-25977
chr10	102753630	102753758	E069	-21447
chr10	102753817	102754682	E069	-20523
chr10	102762046	102762160	E069	-13045
chr10	102762161	102762224	E069	-12981
chr10	102762273	102762339	E069	-12866
chr10	102762356	102762452	E069	-12753
chr10	102762787	102762894	E069	-12311
chr10	102763203	102763315	E069	-11890
chr10	102763320	102763381	E069	-11824
chr10	102763389	102763440	E069	-11765
chr10	102763831	102763900	E069	-11305
chr10	102764020	102764064	E069	-11141
chr10	102764168	102764208	E069	-10997
chr10	102764991	102765072	E069	-10133
chr10	102765153	102765430	E069	-9775
chr10	102765435	102765510	E069	-9695
chr10	102765673	102765723	E069	-9482
chr10	102766095	102766175	E069	-9030
chr10	102766265	102767583	E069	-7622
chr10	102767623	102767754	E069	-7451
chr10	102767799	102767968	E069	-7237
chr10	102768005	102768369	E069	-6836
chr10	102769055	102769113	E069	-6092
chr10	102769124	102769222	E069	-5983
chr10	102769249	102769344	E069	-5861
chr10	102769688	102769738	E069	-5467
chr10	102770493	102770654	E069	-4551
chr10	102771193	102771861	E069	-3344
chr10	102771918	102772010	E069	-3195
chr10	102772016	102772109	E069	-3096
chr10	102772207	102772352	E069	-2853
chr10	102772357	102773586	E069	-1619
chr10	102773844	102774588	E069	-617
chr10	102774628	102775581	E069	0
chr10	102789307	102789697	E069	14102
chr10	102789726	102789900	E069	14521
chr10	102789923	102789988	E069	14718
chr10	102799366	102799497	E069	24161
chr10	102799585	102799668	E069	24380
chr10	102799745	102800261	E069	24540
chr10	102800626	102800764	E069	25421
chr10	102800782	102801260	E069	25577
chr10	102801314	102801422	E069	26109
chr10	102745742	102745889	E070	-29316
chr10	102749666	102749716	E070	-25489
chr10	102762046	102762160	E070	-13045
chr10	102762161	102762224	E070	-12981
chr10	102762273	102762339	E070	-12866
chr10	102762356	102762452	E070	-12753
chr10	102808740	102809378	E070	33535
chr10	102819107	102819436	E070	43902
chr10	102727954	102728353	E071	-46852
chr10	102728355	102728532	E071	-46673
chr10	102745742	102745889	E071	-29316
chr10	102748481	102748633	E071	-26572
chr10	102753630	102753758	E071	-21447
chr10	102753817	102754682	E071	-20523
chr10	102754806	102754934	E071	-20271
chr10	102755016	102755376	E071	-19829
chr10	102755404	102755529	E071	-19676
chr10	102762046	102762160	E071	-13045
chr10	102762161	102762224	E071	-12981
chr10	102762273	102762339	E071	-12866
chr10	102762356	102762452	E071	-12753
chr10	102762787	102762894	E071	-12311
chr10	102763203	102763315	E071	-11890
chr10	102763320	102763381	E071	-11824
chr10	102763389	102763440	E071	-11765
chr10	102763831	102763900	E071	-11305
chr10	102764991	102765072	E071	-10133
chr10	102765153	102765430	E071	-9775
chr10	102765435	102765510	E071	-9695
chr10	102765673	102765723	E071	-9482
chr10	102766095	102766175	E071	-9030
chr10	102766265	102767583	E071	-7622
chr10	102767623	102767754	E071	-7451
chr10	102767799	102767968	E071	-7237
chr10	102768005	102768369	E071	-6836
chr10	102768489	102768915	E071	-6290
chr10	102769055	102769113	E071	-6092
chr10	102769124	102769222	E071	-5983
chr10	102769249	102769344	E071	-5861
chr10	102769688	102769738	E071	-5467
chr10	102771193	102771861	E071	-3344
chr10	102771918	102772010	E071	-3195
chr10	102772207	102772352	E071	-2853
chr10	102773844	102774588	E071	-617
chr10	102799139	102799233	E071	23934
chr10	102799288	102799344	E071	24083
chr10	102799366	102799497	E071	24161
chr10	102799585	102799668	E071	24380
chr10	102799745	102800261	E071	24540
chr10	102800626	102800764	E071	25421
chr10	102800782	102801260	E071	25577
chr10	102801314	102801422	E071	26109
chr10	102801594	102801923	E071	26389
chr10	102728355	102728532	E072	-46673
chr10	102753817	102754682	E072	-20523
chr10	102762046	102762160	E072	-13045
chr10	102762161	102762224	E072	-12981
chr10	102762273	102762339	E072	-12866
chr10	102762356	102762452	E072	-12753
chr10	102762787	102762894	E072	-12311
chr10	102763203	102763315	E072	-11890
chr10	102763320	102763381	E072	-11824
chr10	102763389	102763440	E072	-11765
chr10	102763831	102763900	E072	-11305
chr10	102764991	102765072	E072	-10133
chr10	102765153	102765430	E072	-9775
chr10	102765435	102765510	E072	-9695
chr10	102765673	102765723	E072	-9482
chr10	102766095	102766175	E072	-9030
chr10	102766265	102767583	E072	-7622
chr10	102767623	102767754	E072	-7451
chr10	102767799	102767968	E072	-7237
chr10	102768005	102768369	E072	-6836
chr10	102768489	102768915	E072	-6290
chr10	102769055	102769113	E072	-6092
chr10	102769124	102769222	E072	-5983
chr10	102771193	102771861	E072	-3344
chr10	102771918	102772010	E072	-3195
chr10	102772016	102772109	E072	-3096
chr10	102772207	102772352	E072	-2853
chr10	102772357	102773586	E072	-1619
chr10	102773844	102774588	E072	-617
chr10	102774628	102775581	E072	0
chr10	102788351	102789301	E072	13146
chr10	102789307	102789697	E072	14102
chr10	102799585	102799668	E072	24380
chr10	102799745	102800261	E072	24540
chr10	102728355	102728532	E073	-46673
chr10	102744951	102745050	E073	-30155
chr10	102745289	102745352	E073	-29853
chr10	102745362	102745445	E073	-29760
chr10	102745742	102745889	E073	-29316
chr10	102753817	102754682	E073	-20523
chr10	102762046	102762160	E073	-13045
chr10	102762161	102762224	E073	-12981
chr10	102762273	102762339	E073	-12866
chr10	102762356	102762452	E073	-12753
chr10	102762787	102762894	E073	-12311
chr10	102763203	102763315	E073	-11890
chr10	102763320	102763381	E073	-11824
chr10	102763389	102763440	E073	-11765
chr10	102763831	102763900	E073	-11305
chr10	102766095	102766175	E073	-9030
chr10	102766265	102767583	E073	-7622
chr10	102767623	102767754	E073	-7451
chr10	102767799	102767968	E073	-7237
chr10	102768005	102768369	E073	-6836
chr10	102768489	102768915	E073	-6290
chr10	102769055	102769113	E073	-6092
chr10	102769124	102769222	E073	-5983
chr10	102769249	102769344	E073	-5861
chr10	102771918	102772010	E073	-3195
chr10	102772016	102772109	E073	-3096
chr10	102772207	102772352	E073	-2853
chr10	102772357	102773586	E073	-1619
chr10	102773844	102774588	E073	-617
chr10	102774628	102775581	E073	0
chr10	102788351	102789301	E073	13146
chr10	102728355	102728532	E074	-46673
chr10	102745742	102745889	E074	-29316
chr10	102753630	102753758	E074	-21447
chr10	102753817	102754682	E074	-20523
chr10	102762046	102762160	E074	-13045
chr10	102762161	102762224	E074	-12981
chr10	102762273	102762339	E074	-12866
chr10	102762356	102762452	E074	-12753
chr10	102762787	102762894	E074	-12311
chr10	102763203	102763315	E074	-11890
chr10	102763320	102763381	E074	-11824
chr10	102763389	102763440	E074	-11765
chr10	102763831	102763900	E074	-11305
chr10	102766095	102766175	E074	-9030
chr10	102766265	102767583	E074	-7622
chr10	102767623	102767754	E074	-7451
chr10	102767799	102767968	E074	-7237
chr10	102768005	102768369	E074	-6836
chr10	102769055	102769113	E074	-6092
chr10	102769124	102769222	E074	-5983
chr10	102771193	102771861	E074	-3344
chr10	102771918	102772010	E074	-3195
chr10	102772016	102772109	E074	-3096
chr10	102772207	102772352	E074	-2853
chr10	102772357	102773586	E074	-1619
chr10	102773844	102774588	E074	-617
chr10	102789307	102789697	E074	14102
chr10	102789726	102789900	E074	14521
chr10	102789923	102789988	E074	14718
chr10	102799139	102799233	E074	23934
chr10	102799288	102799344	E074	24083
chr10	102799366	102799497	E074	24161
chr10	102799585	102799668	E074	24380
chr10	102799745	102800261	E074	24540
chr10	102800626	102800764	E074	25421
chr10	102727791	102727838	E081	-47367
chr10	102727954	102728353	E081	-46852
chr10	102728355	102728532	E081	-46673
chr10	102745742	102745889	E081	-29316
chr10	102748481	102748633	E081	-26572
chr10	102753817	102754682	E081	-20523
chr10	102788351	102789301	E081	13146
chr10	102789307	102789697	E081	14102
chr10	102789726	102789900	E081	14521
chr10	102789923	102789988	E081	14718
chr10	102793934	102793978	E081	18729
chr10	102794292	102794629	E081	19087
chr10	102794703	102794743	E081	19498
chr10	102800782	102801260	E081	25577
chr10	102801314	102801422	E081	26109
chr10	102801594	102801923	E081	26389
chr10	102803741	102803795	E081	28536
chr10	102727791	102727838	E082	-47367
chr10	102745742	102745889	E082	-29316
chr10	102749153	102749228	E082	-25977
chr10	102749312	102749367	E082	-25838
chr10	102749378	102749460	E082	-25745
chr10	102749477	102749527	E082	-25678
chr10	102749666	102749716	E082	-25489
chr10	102750224	102750336	E082	-24869
chr10	102750379	102750419	E082	-24786
chr10	102789726	102789900	E082	14521
chr10	102789923	102789988	E082	14718

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr10	102746612	102748063	E067	-27142
chr10	102756074	102761951	E067	-13254
chr10	102789993	102793354	E067	14788
chr10	102746612	102748063	E068	-27142
chr10	102756074	102761951	E068	-13254
chr10	102789993	102793354	E068	14788
chr10	102746612	102748063	E069	-27142
chr10	102756074	102761951	E069	-13254
chr10	102789993	102793354	E069	14788
chr10	102819519	102824151	E069	44314
chr10	102746612	102748063	E070	-27142
chr10	102756074	102761951	E070	-13254
chr10	102789993	102793354	E070	14788
chr10	102746612	102748063	E071	-27142
chr10	102756074	102761951	E071	-13254
chr10	102789993	102793354	E071	14788
chr10	102819519	102824151	E071	44314
chr10	102746612	102748063	E072	-27142
chr10	102756074	102761951	E072	-13254
chr10	102789993	102793354	E072	14788
chr10	102728545	102731770	E073	-43435
chr10	102746612	102748063	E073	-27142
chr10	102756074	102761951	E073	-13254
chr10	102789993	102793354	E073	14788
chr10	102746612	102748063	E074	-27142
chr10	102756074	102761951	E074	-13254
chr10	102789993	102793354	E074	14788
chr10	102746612	102748063	E081	-27142
chr10	102789993	102793354	E081	14788
chr10	102728545	102731770	E082	-43435
chr10	102746612	102748063	E082	-27142
chr10	102756074	102761951	E082	-13254
chr10	102789993	102793354	E082	14788