SNP Detail Info-rs2475335

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.10260263C>T
GRCh37.p13 chr 9	NC_000009.11:g.10260263C>T
PTPRD RefSeqGene	NG_033963.1:g.357461G>A

Gene: PTPRD, protein tyrosine phosphatase, receptor type D(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTPRD transcript variant 1	NM_002839.3:c.	N/A	Intron Variant
PTPRD transcript variant 5	NM_001040712.2:c.	N/A	Genic Upstream Transcript Variant
PTPRD transcript variant 6	NM_001171025.1:c.	N/A	Genic Upstream Transcript Variant
PTPRD transcript variant 2	NM_130391.3:c.	N/A	Genic Upstream Transcript Variant
PTPRD transcript variant 3	NM_130392.3:c.	N/A	Genic Upstream Transcript Variant
PTPRD transcript variant 4	NM_130393.3:c.	N/A	Genic Upstream Transcript Variant
PTPRD transcript variant X10	XM_006716817.3:c.	N/A	Intron Variant
PTPRD transcript variant X24	XM_006716823.2:c.	N/A	Intron Variant
PTPRD transcript variant X26	XM_006716825.3:c.	N/A	Intron Variant
PTPRD transcript variant X28	XM_006716827.3:c.	N/A	Intron Variant
PTPRD transcript variant X40	XM_006716832.3:c.	N/A	Intron Variant
PTPRD transcript variant X41	XM_006716833.3:c.	N/A	Intron Variant
PTPRD transcript variant X42	XM_006716834.3:c.	N/A	Intron Variant
PTPRD transcript variant X45	XM_006716835.3:c.	N/A	Intron Variant
PTPRD transcript variant X48	XM_006716837.3:c.	N/A	Intron Variant
PTPRD transcript variant X49	XM_006716838.3:c.	N/A	Intron Variant
PTPRD transcript variant X50	XM_006716839.3:c.	N/A	Intron Variant
PTPRD transcript variant X25	XM_011517992.2:c.	N/A	Intron Variant
PTPRD transcript variant X1	XM_017014958.1:c.	N/A	Intron Variant
PTPRD transcript variant X2	XM_017014959.1:c.	N/A	Intron Variant
PTPRD transcript variant X3	XM_017014960.1:c.	N/A	Intron Variant
PTPRD transcript variant X4	XM_017014961.1:c.	N/A	Intron Variant
PTPRD transcript variant X6	XM_017014963.1:c.	N/A	Intron Variant
PTPRD transcript variant X7	XM_017014964.1:c.	N/A	Intron Variant
PTPRD transcript variant X8	XM_017014965.1:c.	N/A	Intron Variant
PTPRD transcript variant X9	XM_017014966.1:c.	N/A	Intron Variant
PTPRD transcript variant X11	XM_017014967.1:c.	N/A	Intron Variant
PTPRD transcript variant X12	XM_017014968.1:c.	N/A	Intron Variant
PTPRD transcript variant X13	XM_017014969.1:c.	N/A	Intron Variant
PTPRD transcript variant X14	XM_017014970.1:c.	N/A	Intron Variant
PTPRD transcript variant X15	XM_017014971.1:c.	N/A	Intron Variant
PTPRD transcript variant X16	XM_017014972.1:c.	N/A	Intron Variant
PTPRD transcript variant X17	XM_017014973.1:c.	N/A	Intron Variant
PTPRD transcript variant X18	XM_017014974.1:c.	N/A	Intron Variant
PTPRD transcript variant X19	XM_017014975.1:c.	N/A	Intron Variant
PTPRD transcript variant X20	XM_017014976.1:c.	N/A	Intron Variant
PTPRD transcript variant X21	XM_017014977.1:c.	N/A	Intron Variant
PTPRD transcript variant X22	XM_017014978.1:c.	N/A	Intron Variant
PTPRD transcript variant X23	XM_017014979.1:c.	N/A	Intron Variant
PTPRD transcript variant X27	XM_017014980.1:c.	N/A	Intron Variant
PTPRD transcript variant X29	XM_017014981.1:c.	N/A	Intron Variant
PTPRD transcript variant X30	XM_017014982.1:c.	N/A	Intron Variant
PTPRD transcript variant X31	XM_017014983.1:c.	N/A	Intron Variant
PTPRD transcript variant X32	XM_017014984.1:c.	N/A	Intron Variant
PTPRD transcript variant X33	XM_017014985.1:c.	N/A	Intron Variant
PTPRD transcript variant X34	XM_017014986.1:c.	N/A	Intron Variant
PTPRD transcript variant X35	XM_017014987.1:c.	N/A	Intron Variant
PTPRD transcript variant X36	XM_017014988.1:c.	N/A	Intron Variant
PTPRD transcript variant X37	XM_017014989.1:c.	N/A	Intron Variant
PTPRD transcript variant X38	XM_017014990.1:c.	N/A	Intron Variant
PTPRD transcript variant X39	XM_017014991.1:c.	N/A	Intron Variant
PTPRD transcript variant X43	XM_017014992.1:c.	N/A	Intron Variant
PTPRD transcript variant X44	XM_017014993.1:c.	N/A	Intron Variant
PTPRD transcript variant X46	XM_017014994.1:c.	N/A	Intron Variant
PTPRD transcript variant X47	XM_017014995.1:c.	N/A	Intron Variant
PTPRD transcript variant X5	XM_017014962.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.510	T=0.490
1000Genomes	American	Sub	694	C=0.330	T=0.670
1000Genomes	East Asian	Sub	1008	C=0.201	T=0.799
1000Genomes	Europe	Sub	1006	C=0.193	T=0.807
1000Genomes	Global	Study-wide	5008	C=0.316	T=0.684
1000Genomes	South Asian	Sub	978	C=0.290	T=0.710
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.184	T=0.816
The Genome Aggregation Database	African	Sub	8706	C=0.464	T=0.536
The Genome Aggregation Database	American	Sub	836	C=0.310	T=0.690
The Genome Aggregation Database	East Asian	Sub	1620	C=0.254	T=0.746
The Genome Aggregation Database	Europe	Sub	18478	C=0.187	T=0.812
The Genome Aggregation Database	Global	Study-wide	29942	C=0.275	T=0.724
The Genome Aggregation Database	Other	Sub	302	C=0.250	T=0.750
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.321	T=0.678
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.178	T=0.822

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
rs2475335	0.00076	alcohol dependence	20201924

eQTL of rs2475335 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 rs2475335 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr9	10260352	10260839	E069	89
chr9	10232468	10232728	E070	-27535
chr9	10232775	10232894	E070	-27369
chr9	10232945	10233731	E070	-26532
chr9	10232468	10232728	E071	-27535
chr9	10232775	10232894	E071	-27369
chr9	10232468	10232728	E072	-27535
chr9	10232775	10232894	E072	-27369
chr9	10259748	10259925	E074	-338
chr9	10259981	10260031	E074	-232
chr9	10260152	10260282	E074	0
chr9	10231547	10231600	E081	-28663
chr9	10231625	10231859	E081	-28404
chr9	10232052	10232127	E081	-28136
chr9	10232232	10232385	E081	-27878
chr9	10232468	10232728	E081	-27535
chr9	10232775	10232894	E081	-27369
chr9	10232945	10233731	E081	-26532
chr9	10235225	10235275	E081	-24988
chr9	10235336	10236529	E081	-23734
chr9	10273819	10274255	E081	13556
chr9	10274273	10274457	E081	14010
chr9	10274473	10274667	E081	14210
chr9	10274756	10275259	E081	14493
chr9	10289438	10289488	E081	29175
chr9	10289545	10289595	E081	29282
chr9	10290396	10290526	E081	30133
chr9	10231625	10231859	E082	-28404
chr9	10232052	10232127	E082	-28136
chr9	10232232	10232385	E082	-27878
chr9	10232468	10232728	E082	-27535
chr9	10232775	10232894	E082	-27369
chr9	10232945	10233731	E082	-26532
chr9	10235336	10236529	E082	-23734
chr9	10255335	10255402	E082	-4861
chr9	10255500	10255550	E082	-4713

rs2475335

Genomic Coordinates

Gene: PTPRD, protein tyrosine phosphatase, receptor type D(minus strand)

Population Frequency

P-Value

eQTL of rs2475335 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2475335 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)