rs2014788

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PRDM2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0406 (12166/29946,GnomAD)
C==0350 (10211/29118,TOPMED)
C==0394 (1971/5008,1000G)
T=0483 (1863/3854,ALSPAC)
T=0483 (1790/3708,TWINSUK)

Position: chr1:13799958 (GRCh38.p7) (1p36.21)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 379 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.13799958C>T
GRCh37.p13 chr 1	NC_000001.10:g.14126453C>T

Gene: PRDM2, PR domain 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PRDM2 transcript variant 4	NM_001135610.1:c.	N/A	Intron Variant
PRDM2 transcript variant 1	NM_012231.4:c.	N/A	Intron Variant
PRDM2 transcript variant 3	NM_001007257.2:c.	N/A	Genic Downstream Transcript Variant
PRDM2 transcript variant 2	NM_015866.4:c.	N/A	Genic Downstream Transcript Variant
PRDM2 transcript variant X1	XM_017002253.1:c.	N/A	Intron Variant
PRDM2 transcript variant X2	XM_017002255.1:c.	N/A	Intron Variant
PRDM2 transcript variant X3	XM_017002256.1:c.	N/A	Intron Variant
PRDM2 transcript variant X7	XM_017002258.1:c.	N/A	Intron Variant
PRDM2 transcript variant X8	XM_017002259.1:c.	N/A	Intron Variant
PRDM2 transcript variant X9	XM_017002260.1:c.	N/A	Intron Variant
PRDM2 transcript variant X10	XM_017002261.1:c.	N/A	Intron Variant
PRDM2 transcript variant X12	XM_017002263.1:c.	N/A	Intron Variant
PRDM2 transcript variant X13	XM_017002264.1:c.	N/A	Intron Variant
PRDM2 transcript variant X3	XM_017002254.1:c.	N/A	Genic Downstream Transcript Variant
PRDM2 transcript variant X4	XM_017002257.1:c.	N/A	Genic Downstream Transcript Variant
PRDM2 transcript variant X8	XM_017002262.1:c.	N/A	Genic Downstream Transcript Variant
PRDM2 transcript variant X2	XR_001737400.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.058	T=0.942
1000Genomes	American	Sub	694	C=0.390	T=0.610
1000Genomes	East Asian	Sub	1008	C=0.438	T=0.562
1000Genomes	Europe	Sub	1006	C=0.492	T=0.508
1000Genomes	Global	Study-wide	5008	C=0.394	T=0.606
1000Genomes	South Asian	Sub	978	C=0.700	T=0.300
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.517	T=0.483
The Genome Aggregation Database	African	Sub	8718	C=0.113	T=0.887
The Genome Aggregation Database	American	Sub	838	C=0.430	T=0.570
The Genome Aggregation Database	East Asian	Sub	1620	C=0.400	T=0.600
The Genome Aggregation Database	Europe	Sub	18470	C=0.542	T=0.457
The Genome Aggregation Database	Global	Study-wide	29946	C=0.406	T=0.593
The Genome Aggregation Database	Other	Sub	300	C=0.490	T=0.510
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.350	T=0.649
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.517	T=0.483

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
rs2014788	0.000963	alcohol dependence	20201924

eQTL of rs2014788 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 rs2014788 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	14079574	14079628	E067	-46825
chr1	14079675	14079746	E067	-46707
chr1	14079803	14079853	E067	-46600
chr1	14079971	14080031	E067	-46422
chr1	14080256	14080415	E067	-46038
chr1	14080433	14080663	E067	-45790
chr1	14081317	14081533	E067	-44920
chr1	14083189	14083268	E067	-43185
chr1	14083337	14083430	E067	-43023
chr1	14083835	14083885	E067	-42568
chr1	14086774	14086824	E067	-39629
chr1	14086852	14086902	E067	-39551
chr1	14086941	14087122	E067	-39331
chr1	14087222	14087290	E067	-39163
chr1	14087499	14087676	E067	-38777
chr1	14088076	14088204	E067	-38249
chr1	14088569	14088761	E067	-37692
chr1	14088842	14089244	E067	-37209
chr1	14089279	14089327	E067	-37126
chr1	14089347	14089420	E067	-37033
chr1	14089534	14089592	E067	-36861
chr1	14089628	14089668	E067	-36785
chr1	14089682	14090069	E067	-36384
chr1	14090106	14090224	E067	-36229
chr1	14090485	14090535	E067	-35918
chr1	14090631	14090756	E067	-35697
chr1	14090998	14091510	E067	-34943
chr1	14091541	14091734	E067	-34719
chr1	14098440	14098555	E067	-27898
chr1	14098708	14099119	E067	-27334
chr1	14101483	14101662	E067	-24791
chr1	14102024	14102288	E067	-24165
chr1	14106273	14106322	E067	-20131
chr1	14106462	14106711	E067	-19742
chr1	14107913	14107998	E067	-18455
chr1	14108275	14108324	E067	-18129
chr1	14108409	14109155	E067	-17298
chr1	14109238	14109386	E067	-17067
chr1	14109628	14109717	E067	-16736
chr1	14109919	14110126	E067	-16327
chr1	14110153	14110358	E067	-16095
chr1	14116644	14116758	E067	-9695
chr1	14116915	14116977	E067	-9476
chr1	14117288	14117342	E067	-9111
chr1	14117415	14117531	E067	-8922
chr1	14117887	14117974	E067	-8479
chr1	14118289	14118343	E067	-8110
chr1	14118347	14118397	E067	-8056
chr1	14118431	14118493	E067	-7960
chr1	14118510	14118564	E067	-7889
chr1	14118938	14119207	E067	-7246
chr1	14119235	14119285	E067	-7168
chr1	14127480	14127653	E067	1027
chr1	14127744	14127862	E067	1291
chr1	14127886	14128586	E067	1433
chr1	14133825	14133967	E067	7372
chr1	14135382	14135575	E067	8929
chr1	14135702	14135760	E067	9249
chr1	14077838	14077918	E068	-48535
chr1	14078078	14078378	E068	-48075
chr1	14079574	14079628	E068	-46825
chr1	14079675	14079746	E068	-46707
chr1	14079803	14079853	E068	-46600
chr1	14079971	14080031	E068	-46422
chr1	14080256	14080415	E068	-46038
chr1	14080433	14080663	E068	-45790
chr1	14080820	14080956	E068	-45497
chr1	14081317	14081533	E068	-44920
chr1	14083189	14083268	E068	-43185
chr1	14083337	14083430	E068	-43023
chr1	14083835	14083885	E068	-42568
chr1	14084322	14084688	E068	-41765
chr1	14085563	14086094	E068	-40359
chr1	14086774	14086824	E068	-39629
chr1	14086852	14086902	E068	-39551
chr1	14086941	14087122	E068	-39331
chr1	14087222	14087290	E068	-39163
chr1	14087499	14087676	E068	-38777
chr1	14088076	14088204	E068	-38249
chr1	14088569	14088761	E068	-37692
chr1	14088842	14089244	E068	-37209
chr1	14089279	14089327	E068	-37126
chr1	14089347	14089420	E068	-37033
chr1	14089534	14089592	E068	-36861
chr1	14089628	14089668	E068	-36785
chr1	14089682	14090069	E068	-36384
chr1	14090106	14090224	E068	-36229
chr1	14090485	14090535	E068	-35918
chr1	14090631	14090756	E068	-35697
chr1	14090998	14091510	E068	-34943
chr1	14091541	14091734	E068	-34719
chr1	14098440	14098555	E068	-27898
chr1	14098708	14099119	E068	-27334
chr1	14102523	14102798	E068	-23655
chr1	14107913	14107998	E068	-18455
chr1	14108275	14108324	E068	-18129
chr1	14108409	14109155	E068	-17298
chr1	14113147	14113238	E068	-13215
chr1	14118431	14118493	E068	-7960
chr1	14118510	14118564	E068	-7889
chr1	14118938	14119207	E068	-7246
chr1	14119235	14119285	E068	-7168
chr1	14077838	14077918	E069	-48535
chr1	14079574	14079628	E069	-46825
chr1	14079675	14079746	E069	-46707
chr1	14079803	14079853	E069	-46600
chr1	14079971	14080031	E069	-46422
chr1	14080256	14080415	E069	-46038
chr1	14080433	14080663	E069	-45790
chr1	14080820	14080956	E069	-45497
chr1	14081317	14081533	E069	-44920
chr1	14083189	14083268	E069	-43185
chr1	14083337	14083430	E069	-43023
chr1	14083835	14083885	E069	-42568
chr1	14084322	14084688	E069	-41765
chr1	14085563	14086094	E069	-40359
chr1	14086774	14086824	E069	-39629
chr1	14086852	14086902	E069	-39551
chr1	14086941	14087122	E069	-39331
chr1	14087222	14087290	E069	-39163
chr1	14087499	14087676	E069	-38777
chr1	14088076	14088204	E069	-38249
chr1	14088569	14088761	E069	-37692
chr1	14089534	14089592	E069	-36861
chr1	14089628	14089668	E069	-36785
chr1	14089682	14090069	E069	-36384
chr1	14090106	14090224	E069	-36229
chr1	14090485	14090535	E069	-35918
chr1	14090631	14090756	E069	-35697
chr1	14090998	14091510	E069	-34943
chr1	14091541	14091734	E069	-34719
chr1	14092815	14092897	E069	-33556
chr1	14097717	14097757	E069	-28696
chr1	14098440	14098555	E069	-27898
chr1	14101483	14101662	E069	-24791
chr1	14102024	14102288	E069	-24165
chr1	14105548	14105628	E069	-20825
chr1	14106273	14106322	E069	-20131
chr1	14106462	14106711	E069	-19742
chr1	14106870	14106922	E069	-19531
chr1	14107312	14107411	E069	-19042
chr1	14107651	14107718	E069	-18735
chr1	14107913	14107998	E069	-18455
chr1	14108275	14108324	E069	-18129
chr1	14108409	14109155	E069	-17298
chr1	14113147	14113238	E069	-13215
chr1	14115437	14115532	E069	-10921
chr1	14126444	14126595	E069	0
chr1	14127102	14127156	E069	649
chr1	14127330	14127388	E069	877
chr1	14127480	14127653	E069	1027
chr1	14127744	14127862	E069	1291
chr1	14133825	14133967	E069	7372
chr1	14078078	14078378	E070	-48075
chr1	14078635	14078788	E070	-47665
chr1	14081317	14081533	E070	-44920
chr1	14088076	14088204	E070	-38249
chr1	14088569	14088761	E070	-37692
chr1	14088842	14089244	E070	-37209
chr1	14089279	14089327	E070	-37126
chr1	14089347	14089420	E070	-37033
chr1	14089534	14089592	E070	-36861
chr1	14089628	14089668	E070	-36785
chr1	14089682	14090069	E070	-36384
chr1	14090106	14090224	E070	-36229
chr1	14090485	14090535	E070	-35918
chr1	14090631	14090756	E070	-35697
chr1	14077838	14077918	E071	-48535
chr1	14078078	14078378	E071	-48075
chr1	14079574	14079628	E071	-46825
chr1	14079675	14079746	E071	-46707
chr1	14079803	14079853	E071	-46600
chr1	14079971	14080031	E071	-46422
chr1	14080256	14080415	E071	-46038
chr1	14080433	14080663	E071	-45790
chr1	14080820	14080956	E071	-45497
chr1	14081317	14081533	E071	-44920
chr1	14083189	14083268	E071	-43185
chr1	14083337	14083430	E071	-43023
chr1	14083835	14083885	E071	-42568
chr1	14084322	14084688	E071	-41765
chr1	14085563	14086094	E071	-40359
chr1	14086774	14086824	E071	-39629
chr1	14086852	14086902	E071	-39551
chr1	14086941	14087122	E071	-39331
chr1	14087222	14087290	E071	-39163
chr1	14087499	14087676	E071	-38777
chr1	14088076	14088204	E071	-38249
chr1	14089628	14089668	E071	-36785
chr1	14089682	14090069	E071	-36384
chr1	14090106	14090224	E071	-36229
chr1	14090485	14090535	E071	-35918
chr1	14090631	14090756	E071	-35697
chr1	14090998	14091510	E071	-34943
chr1	14091541	14091734	E071	-34719
chr1	14092815	14092897	E071	-33556
chr1	14098440	14098555	E071	-27898
chr1	14098708	14099119	E071	-27334
chr1	14106462	14106711	E071	-19742
chr1	14106870	14106922	E071	-19531
chr1	14108275	14108324	E071	-18129
chr1	14108409	14109155	E071	-17298
chr1	14113147	14113238	E071	-13215
chr1	14116644	14116758	E071	-9695
chr1	14116915	14116977	E071	-9476
chr1	14117288	14117342	E071	-9111
chr1	14117415	14117531	E071	-8922
chr1	14126938	14126987	E071	485
chr1	14127102	14127156	E071	649
chr1	14127330	14127388	E071	877
chr1	14127480	14127653	E071	1027
chr1	14127744	14127862	E071	1291
chr1	14079574	14079628	E072	-46825
chr1	14079675	14079746	E072	-46707
chr1	14079803	14079853	E072	-46600
chr1	14079971	14080031	E072	-46422
chr1	14080256	14080415	E072	-46038
chr1	14080433	14080663	E072	-45790
chr1	14080820	14080956	E072	-45497
chr1	14083189	14083268	E072	-43185
chr1	14083337	14083430	E072	-43023
chr1	14083835	14083885	E072	-42568
chr1	14084322	14084688	E072	-41765
chr1	14084796	14084846	E072	-41607
chr1	14084974	14085047	E072	-41406
chr1	14085563	14086094	E072	-40359
chr1	14086774	14086824	E072	-39629
chr1	14086852	14086902	E072	-39551
chr1	14086941	14087122	E072	-39331
chr1	14087222	14087290	E072	-39163
chr1	14087499	14087676	E072	-38777
chr1	14088076	14088204	E072	-38249
chr1	14089534	14089592	E072	-36861
chr1	14089628	14089668	E072	-36785
chr1	14089682	14090069	E072	-36384
chr1	14090106	14090224	E072	-36229
chr1	14090485	14090535	E072	-35918
chr1	14090631	14090756	E072	-35697
chr1	14090998	14091510	E072	-34943
chr1	14091541	14091734	E072	-34719
chr1	14095825	14095915	E072	-30538
chr1	14098440	14098555	E072	-27898
chr1	14098708	14099119	E072	-27334
chr1	14102024	14102288	E072	-24165
chr1	14106462	14106711	E072	-19742
chr1	14106870	14106922	E072	-19531
chr1	14107651	14107718	E072	-18735
chr1	14107913	14107998	E072	-18455
chr1	14108275	14108324	E072	-18129
chr1	14108409	14109155	E072	-17298
chr1	14113147	14113238	E072	-13215
chr1	14116644	14116758	E072	-9695
chr1	14116915	14116977	E072	-9476
chr1	14119235	14119285	E072	-7168
chr1	14133825	14133967	E072	7372
chr1	14135042	14135117	E072	8589
chr1	14135382	14135575	E072	8929
chr1	14135702	14135760	E072	9249
chr1	14079574	14079628	E073	-46825
chr1	14079675	14079746	E073	-46707
chr1	14079803	14079853	E073	-46600
chr1	14079971	14080031	E073	-46422
chr1	14080256	14080415	E073	-46038
chr1	14080433	14080663	E073	-45790
chr1	14080820	14080956	E073	-45497
chr1	14081317	14081533	E073	-44920
chr1	14083835	14083885	E073	-42568
chr1	14086852	14086902	E073	-39551
chr1	14086941	14087122	E073	-39331
chr1	14087222	14087290	E073	-39163
chr1	14088569	14088761	E073	-37692
chr1	14089534	14089592	E073	-36861
chr1	14089628	14089668	E073	-36785
chr1	14089682	14090069	E073	-36384
chr1	14090998	14091510	E073	-34943
chr1	14091541	14091734	E073	-34719
chr1	14092815	14092897	E073	-33556
chr1	14095825	14095915	E073	-30538
chr1	14095978	14096065	E073	-30388
chr1	14106462	14106711	E073	-19742
chr1	14106870	14106922	E073	-19531
chr1	14109919	14110126	E073	-16327
chr1	14110153	14110358	E073	-16095
chr1	14110842	14110892	E073	-15561
chr1	14110944	14111088	E073	-15365
chr1	14111106	14111201	E073	-15252
chr1	14113147	14113238	E073	-13215
chr1	14116644	14116758	E073	-9695
chr1	14116915	14116977	E073	-9476
chr1	14117288	14117342	E073	-9111
chr1	14117415	14117531	E073	-8922
chr1	14119235	14119285	E073	-7168
chr1	14126938	14126987	E073	485
chr1	14127102	14127156	E073	649
chr1	14127330	14127388	E073	877
chr1	14127480	14127653	E073	1027
chr1	14127744	14127862	E073	1291
chr1	14127886	14128586	E073	1433
chr1	14129266	14129356	E073	2813
chr1	14129394	14129479	E073	2941
chr1	14133825	14133967	E073	7372
chr1	14077838	14077918	E074	-48535
chr1	14078078	14078378	E074	-48075
chr1	14079574	14079628	E074	-46825
chr1	14079675	14079746	E074	-46707
chr1	14079803	14079853	E074	-46600
chr1	14079971	14080031	E074	-46422
chr1	14080256	14080415	E074	-46038
chr1	14080433	14080663	E074	-45790
chr1	14080820	14080956	E074	-45497
chr1	14081317	14081533	E074	-44920
chr1	14083189	14083268	E074	-43185
chr1	14083337	14083430	E074	-43023
chr1	14083835	14083885	E074	-42568
chr1	14084322	14084688	E074	-41765
chr1	14084796	14084846	E074	-41607
chr1	14085563	14086094	E074	-40359
chr1	14086774	14086824	E074	-39629
chr1	14086852	14086902	E074	-39551
chr1	14086941	14087122	E074	-39331
chr1	14087222	14087290	E074	-39163
chr1	14087499	14087676	E074	-38777
chr1	14088076	14088204	E074	-38249
chr1	14088569	14088761	E074	-37692
chr1	14088842	14089244	E074	-37209
chr1	14089279	14089327	E074	-37126
chr1	14089347	14089420	E074	-37033
chr1	14089534	14089592	E074	-36861
chr1	14089628	14089668	E074	-36785
chr1	14089682	14090069	E074	-36384
chr1	14090106	14090224	E074	-36229
chr1	14090485	14090535	E074	-35918
chr1	14090631	14090756	E074	-35697
chr1	14090998	14091510	E074	-34943
chr1	14091541	14091734	E074	-34719
chr1	14097717	14097757	E074	-28696
chr1	14098440	14098555	E074	-27898
chr1	14106462	14106711	E074	-19742
chr1	14106870	14106922	E074	-19531
chr1	14108409	14109155	E074	-17298
chr1	14109238	14109386	E074	-17067
chr1	14109628	14109717	E074	-16736
chr1	14109919	14110126	E074	-16327
chr1	14110153	14110358	E074	-16095
chr1	14113147	14113238	E074	-13215
chr1	14077838	14077918	E081	-48535
chr1	14078078	14078378	E081	-48075
chr1	14078635	14078788	E081	-47665
chr1	14088842	14089244	E081	-37209
chr1	14089279	14089327	E081	-37126
chr1	14090998	14091510	E081	-34943
chr1	14092815	14092897	E081	-33556
chr1	14093186	14093779	E081	-32674
chr1	14117288	14117342	E081	-9111
chr1	14117415	14117531	E081	-8922
chr1	14117887	14117974	E081	-8479
chr1	14118289	14118343	E081	-8110
chr1	14118347	14118397	E081	-8056
chr1	14118431	14118493	E081	-7960
chr1	14118510	14118564	E081	-7889
chr1	14118938	14119207	E081	-7246
chr1	14119235	14119285	E081	-7168
chr1	14127744	14127862	E081	1291
chr1	14127886	14128586	E081	1433
chr1	14077838	14077918	E082	-48535
chr1	14078078	14078378	E082	-48075
chr1	14078635	14078788	E082	-47665
chr1	14083189	14083268	E082	-43185
chr1	14083337	14083430	E082	-43023
chr1	14083835	14083885	E082	-42568
chr1	14088842	14089244	E082	-37209
chr1	14089279	14089327	E082	-37126
chr1	14089347	14089420	E082	-37033
chr1	14089534	14089592	E082	-36861
chr1	14089628	14089668	E082	-36785
chr1	14090106	14090224	E082	-36229
chr1	14117288	14117342	E082	-9111
chr1	14117415	14117531	E082	-8922
chr1	14119235	14119285	E082	-7168

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	14076938	14077223	E067	-49230
chr1	14076938	14077223	E068	-49230
chr1	14076938	14077223	E069	-49230
chr1	14076938	14077223	E070	-49230
chr1	14076938	14077223	E071	-49230
chr1	14076938	14077223	E072	-49230
chr1	14076938	14077223	E073	-49230
chr1	14076938	14077223	E074	-49230
chr1	14076938	14077223	E082	-49230