rs34892520

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

POLR1A : Missense Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0078 (9514/120768,ExAC)
T=0097 (2917/29958,GnomAD)
T=0114 (3338/29116,TOPMED)
C==0098 (1194/12152,GO-ESP)
T=0102 (512/5008,1000G)
T=0066 (253/3854,ALSPAC)
T=0064 (237/3708,TWINSUK)

Position: chr2:86042040 (GRCh38.p7) (2p11.2)

Phenotype: CD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 221 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.86042040C>T
GRCh37.p13 chr 2	NC_000002.11:g.86269163C>T

Gene: POLR1A, polymerase (RNA) I subunit A(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
POLR1A transcript	NM_015425.3:c.342...NM_015425.3:c.3421G>A	A [GCT]> T [ACT]	Coding Sequence Variant
DNA-directed RNA polymerase I subunit RPA1	NP_056240.2:p.Ala...NP_056240.2:p.Ala1141Thr	A [Ala]> T [Thr]	Missense Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.809	T=0.191
1000Genomes	American	Sub	694	C=0.900	T=0.100
1000Genomes	East Asian	Sub	1008	C=0.978	T=0.022
1000Genomes	Europe	Sub	1006	C=0.934	T=0.066
1000Genomes	Global	Study-wide	5008	C=0.898	T=0.102
1000Genomes	South Asian	Sub	978	C=0.900	T=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.934	T=0.066
The Exome Aggregation Consortium	American	Sub	21378	C=0.871	T=0.128
The Exome Aggregation Consortium	Asian	Sub	25138	C=0.918	T=0.082
The Exome Aggregation Consortium	Europe	Sub	73352	C=0.936	T=0.063
The Exome Aggregation Consortium	Global	Study-wide	120768	C=0.921	T=0.078
The Exome Aggregation Consortium	Other	Sub	900	C=0.920	T=0.080
The Genome Aggregation Database	African	Sub	8722	C=0.809	T=0.191
The Genome Aggregation Database	American	Sub	838	C=0.910	T=0.090
The Genome Aggregation Database	East Asian	Sub	1620	C=0.980	T=0.020
The Genome Aggregation Database	Europe	Sub	18480	C=0.939	T=0.060
The Genome Aggregation Database	Global	Study-wide	29958	C=0.902	T=0.097
The Genome Aggregation Database	Other	Sub	298	C=0.890	T=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.885	T=0.114
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.936	T=0.064

PMID	Title	Author	Journal
23958962	Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.	Gelernter J	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs34892520	0.000699	cocaine dependence	23958962

eQTL of rs34892520 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:86269163	POLR1A	ENSG00000068654.11	C>T	1.2643e-12	-64115	Cerebellum
Chr2:86269163	MRPL35	ENSG00000132313.10	C>T	9.3003e-10	-157315	Cerebellum
Chr2:86269163	POLR1A	ENSG00000068654.11	C>T	8.7150e-7	-64115	Cortex
Chr2:86269163	RP11-301O19.1	ENSG00000273080.1	C>T	6.1741e-8	-153731	Cortex
Chr2:86269163	POLR1A	ENSG00000068654.11	C>T	2.2452e-13	-64115	Cerebellar_Hemisphere
Chr2:86269163	MRPL35	ENSG00000132313.10	C>T	4.3418e-5	-157315	Cerebellar_Hemisphere
Chr2:86269163	POLR1A	ENSG00000068654.11	C>T	7.6238e-5	-64115	Caudate_basal_ganglia
Chr2:86269163	POLR1A	ENSG00000068654.11	C>T	7.8075e-6	-64115	Putamen_basal_ganglia
Chr2:86269163	POLR1A	ENSG00000068654.11	C>T	1.1754e-5	-64115	Nucleus_accumbens_basal_ganglia

meQTL of rs34892520 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 )
chr2	86223673	86224071	E067	-45092
chr2	86224192	86224498	E067	-44665
chr2	86224574	86224676	E067	-44487
chr2	86225257	86226705	E067	-42458
chr2	86226720	86226909	E067	-42254
chr2	86244895	86244957	E067	-24206
chr2	86245069	86245260	E067	-23903
chr2	86245305	86245442	E067	-23721
chr2	86245771	86246008	E067	-23155
chr2	86247851	86247899	E067	-21264
chr2	86247938	86247995	E067	-21168
chr2	86248147	86248426	E067	-20737
chr2	86248459	86248601	E067	-20562
chr2	86248608	86248794	E067	-20369
chr2	86248960	86249043	E067	-20120
chr2	86249237	86249413	E067	-19750
chr2	86253251	86253397	E067	-15766
chr2	86253473	86253921	E067	-15242
chr2	86262377	86266953	E067	-2210
chr2	86292383	86292427	E067	23220
chr2	86295274	86295703	E067	26111
chr2	86299208	86299293	E067	30045
chr2	86299329	86300128	E067	30166
chr2	86222630	86222680	E068	-46483
chr2	86222896	86222948	E068	-46215
chr2	86223201	86223306	E068	-45857
chr2	86223673	86224071	E068	-45092
chr2	86224192	86224498	E068	-44665
chr2	86224574	86224676	E068	-44487
chr2	86225257	86226705	E068	-42458
chr2	86226720	86226909	E068	-42254
chr2	86244895	86244957	E068	-24206
chr2	86245069	86245260	E068	-23903
chr2	86245305	86245442	E068	-23721
chr2	86245771	86246008	E068	-23155
chr2	86247851	86247899	E068	-21264
chr2	86247938	86247995	E068	-21168
chr2	86248147	86248426	E068	-20737
chr2	86248459	86248601	E068	-20562
chr2	86248608	86248794	E068	-20369
chr2	86248960	86249043	E068	-20120
chr2	86252494	86252607	E068	-16556
chr2	86253251	86253397	E068	-15766
chr2	86253473	86253921	E068	-15242
chr2	86262377	86266953	E068	-2210
chr2	86274538	86274592	E068	5375
chr2	86299063	86299142	E068	29900
chr2	86299208	86299293	E068	30045
chr2	86299329	86300128	E068	30166
chr2	86305906	86306217	E068	36743
chr2	86306236	86306272	E068	37073
chr2	86306398	86306503	E068	37235
chr2	86306536	86306675	E068	37373
chr2	86221713	86221773	E069	-47390
chr2	86222057	86222197	E069	-46966
chr2	86222408	86222560	E069	-46603
chr2	86222630	86222680	E069	-46483
chr2	86222896	86222948	E069	-46215
chr2	86223201	86223306	E069	-45857
chr2	86223673	86224071	E069	-45092
chr2	86224192	86224498	E069	-44665
chr2	86224574	86224676	E069	-44487
chr2	86225257	86226705	E069	-42458
chr2	86226720	86226909	E069	-42254
chr2	86227453	86227584	E069	-41579
chr2	86244118	86244635	E069	-24528
chr2	86244895	86244957	E069	-24206
chr2	86245069	86245260	E069	-23903
chr2	86245305	86245442	E069	-23721
chr2	86245771	86246008	E069	-23155
chr2	86247851	86247899	E069	-21264
chr2	86247938	86247995	E069	-21168
chr2	86248147	86248426	E069	-20737
chr2	86248459	86248601	E069	-20562
chr2	86248608	86248794	E069	-20369
chr2	86248960	86249043	E069	-20120
chr2	86249237	86249413	E069	-19750
chr2	86252494	86252607	E069	-16556
chr2	86253251	86253397	E069	-15766
chr2	86253473	86253921	E069	-15242
chr2	86254392	86254612	E069	-14551
chr2	86254769	86254864	E069	-14299
chr2	86255052	86255110	E069	-14053
chr2	86255253	86255579	E069	-13584
chr2	86262377	86266953	E069	-2210
chr2	86299063	86299142	E069	29900
chr2	86299208	86299293	E069	30045
chr2	86299329	86300128	E069	30166
chr2	86300415	86300496	E069	31252
chr2	86262377	86266953	E070	-2210
chr2	86221107	86221511	E071	-47652
chr2	86221713	86221773	E071	-47390
chr2	86222057	86222197	E071	-46966
chr2	86222408	86222560	E071	-46603
chr2	86222630	86222680	E071	-46483
chr2	86222896	86222948	E071	-46215
chr2	86223201	86223306	E071	-45857
chr2	86223673	86224071	E071	-45092
chr2	86224192	86224498	E071	-44665
chr2	86224574	86224676	E071	-44487
chr2	86225257	86226705	E071	-42458
chr2	86226720	86226909	E071	-42254
chr2	86227453	86227584	E071	-41579
chr2	86227788	86227859	E071	-41304
chr2	86227862	86227932	E071	-41231
chr2	86227964	86228195	E071	-40968
chr2	86244118	86244635	E071	-24528
chr2	86244895	86244957	E071	-24206
chr2	86245069	86245260	E071	-23903
chr2	86245305	86245442	E071	-23721
chr2	86245771	86246008	E071	-23155
chr2	86246054	86246211	E071	-22952
chr2	86247851	86247899	E071	-21264
chr2	86247938	86247995	E071	-21168
chr2	86248147	86248426	E071	-20737
chr2	86248459	86248601	E071	-20562
chr2	86248608	86248794	E071	-20369
chr2	86248960	86249043	E071	-20120
chr2	86249237	86249413	E071	-19750
chr2	86252494	86252607	E071	-16556
chr2	86253251	86253397	E071	-15766
chr2	86253473	86253921	E071	-15242
chr2	86254392	86254612	E071	-14551
chr2	86254769	86254864	E071	-14299
chr2	86255052	86255110	E071	-14053
chr2	86255253	86255579	E071	-13584
chr2	86255712	86256302	E071	-12861
chr2	86256343	86256394	E071	-12769
chr2	86262377	86266953	E071	-2210
chr2	86295797	86296259	E071	26634
chr2	86299063	86299142	E071	29900
chr2	86299208	86299293	E071	30045
chr2	86299329	86300128	E071	30166
chr2	86306398	86306503	E071	37235
chr2	86306536	86306675	E071	37373
chr2	86306731	86306810	E071	37568
chr2	86223201	86223306	E072	-45857
chr2	86223673	86224071	E072	-45092
chr2	86224192	86224498	E072	-44665
chr2	86224574	86224676	E072	-44487
chr2	86225257	86226705	E072	-42458
chr2	86226720	86226909	E072	-42254
chr2	86243897	86244113	E072	-25050
chr2	86245069	86245260	E072	-23903
chr2	86245305	86245442	E072	-23721
chr2	86245771	86246008	E072	-23155
chr2	86246054	86246211	E072	-22952
chr2	86246212	86246262	E072	-22901
chr2	86246284	86246385	E072	-22778
chr2	86247851	86247899	E072	-21264
chr2	86247938	86247995	E072	-21168
chr2	86248147	86248426	E072	-20737
chr2	86248459	86248601	E072	-20562
chr2	86248608	86248794	E072	-20369
chr2	86248960	86249043	E072	-20120
chr2	86252494	86252607	E072	-16556
chr2	86253251	86253397	E072	-15766
chr2	86253473	86253921	E072	-15242
chr2	86262377	86266953	E072	-2210
chr2	86299063	86299142	E072	29900
chr2	86299208	86299293	E072	30045
chr2	86299329	86300128	E072	30166
chr2	86306236	86306272	E072	37073
chr2	86307008	86308072	E072	37845
chr2	86223201	86223306	E073	-45857
chr2	86223673	86224071	E073	-45092
chr2	86224192	86224498	E073	-44665
chr2	86224574	86224676	E073	-44487
chr2	86225257	86226705	E073	-42458
chr2	86226720	86226909	E073	-42254
chr2	86244895	86244957	E073	-24206
chr2	86245069	86245260	E073	-23903
chr2	86245305	86245442	E073	-23721
chr2	86245771	86246008	E073	-23155
chr2	86247851	86247899	E073	-21264
chr2	86247938	86247995	E073	-21168
chr2	86248147	86248426	E073	-20737
chr2	86248459	86248601	E073	-20562
chr2	86248608	86248794	E073	-20369
chr2	86248960	86249043	E073	-20120
chr2	86249237	86249413	E073	-19750
chr2	86252494	86252607	E073	-16556
chr2	86253251	86253397	E073	-15766
chr2	86253473	86253921	E073	-15242
chr2	86262377	86266953	E073	-2210
chr2	86272773	86273028	E073	3610
chr2	86299063	86299142	E073	29900
chr2	86299208	86299293	E073	30045
chr2	86299329	86300128	E073	30166
chr2	86307008	86308072	E073	37845
chr2	86223201	86223306	E074	-45857
chr2	86223673	86224071	E074	-45092
chr2	86224192	86224498	E074	-44665
chr2	86224574	86224676	E074	-44487
chr2	86225257	86226705	E074	-42458
chr2	86228476	86228543	E074	-40620
chr2	86244895	86244957	E074	-24206
chr2	86245069	86245260	E074	-23903
chr2	86245305	86245442	E074	-23721
chr2	86245771	86246008	E074	-23155
chr2	86246054	86246211	E074	-22952
chr2	86246212	86246262	E074	-22901
chr2	86246284	86246385	E074	-22778
chr2	86247851	86247899	E074	-21264
chr2	86247938	86247995	E074	-21168
chr2	86248147	86248426	E074	-20737
chr2	86248459	86248601	E074	-20562
chr2	86248608	86248794	E074	-20369
chr2	86248960	86249043	E074	-20120
chr2	86249237	86249413	E074	-19750
chr2	86252494	86252607	E074	-16556
chr2	86253251	86253397	E074	-15766
chr2	86253473	86253921	E074	-15242
chr2	86262377	86266953	E074	-2210
chr2	86299063	86299142	E074	29900
chr2	86299208	86299293	E074	30045
chr2	86299329	86300128	E074	30166
chr2	86224192	86224498	E081	-44665
chr2	86224574	86224676	E081	-44487
chr2	86225257	86226705	E081	-42458
chr2	86223673	86224071	E082	-45092