SNP Detail Info-rs12001948

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.8320837G>C
GRCh37.p13 chr 9	NC_000009.11:g.8320837G>C
PTPRD RefSeqGene	NG_033963.1:g.2296887C>G

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

Molecule type	Change	Amino acid[Codon]	SO Term
PTPRD transcript variant 5	NM_001040712.2:c.	N/A	Intron Variant
PTPRD transcript variant 6	NM_001171025.1:c.	N/A	Intron Variant
PTPRD transcript variant 1	NM_002839.3:c.	N/A	Intron Variant
PTPRD transcript variant 2	NM_130391.3:c.	N/A	Intron Variant
PTPRD transcript variant 3	NM_130392.3:c.	N/A	Intron Variant
PTPRD transcript variant 4	NM_130393.3:c.	N/A	Intron 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 X5	XM_017014962.1: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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.938	C=0.062
1000Genomes	American	Sub	694	G=0.990	C=0.010
1000Genomes	East Asian	Sub	1008	G=1.000	C=0.000
1000Genomes	Europe	Sub	1006	G=1.000	C=0.000
1000Genomes	Global	Study-wide	5008	G=0.982	C=0.018
1000Genomes	South Asian	Sub	978	G=1.000	C=0.000
The Genome Aggregation Database	African	Sub	8720	G=0.947	C=0.053
The Genome Aggregation Database	American	Sub	838	G=1.000	C=0.000
The Genome Aggregation Database	East Asian	Sub	1594	G=1.000	C=0.000
The Genome Aggregation Database	Europe	Sub	18502	G=0.999	C=0.000
The Genome Aggregation Database	Global	Study-wide	29956	G=0.984	C=0.015
The Genome Aggregation Database	Other	Sub	302	G=1.000	C=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.974	C=0.025

PMID	Title	Author	Journal
17407593	Molecular genetics of nicotine dependence and abstinence: whole genome association using 520,000 SNPs.	Uhl GR	BMC Genet

P-Value

SNP ID	p-value	Traits	Study
rs12001948	0.00047	nicotine dependence	17407593

eQTL of rs12001948 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 rs12001948 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	8348714	8348771	E067	27877
chr9	8363574	8363628	E067	42737
chr9	8363887	8363995	E067	43050
chr9	8364076	8364656	E067	43239
chr9	8365067	8365360	E067	44230
chr9	8365067	8365360	E068	44230
chr9	8315322	8315489	E069	-5348
chr9	8315552	8315602	E069	-5235
chr9	8318454	8318611	E069	-2226
chr9	8348714	8348771	E069	27877
chr9	8348801	8348851	E069	27964
chr9	8348907	8349003	E069	28070
chr9	8349230	8349896	E069	28393
chr9	8350033	8350286	E069	29196
chr9	8350296	8350367	E069	29459
chr9	8352003	8352215	E069	31166
chr9	8352289	8352339	E069	31452
chr9	8363887	8363995	E069	43050
chr9	8365067	8365360	E069	44230
chr9	8365517	8365902	E069	44680
chr9	8284980	8285111	E070	-35726
chr9	8285358	8285440	E070	-35397
chr9	8364076	8364656	E070	43239
chr9	8318454	8318611	E071	-2226
chr9	8347509	8347559	E071	26672
chr9	8348714	8348771	E071	27877
chr9	8348801	8348851	E071	27964
chr9	8348907	8349003	E071	28070
chr9	8349230	8349896	E071	28393
chr9	8350033	8350286	E071	29196
chr9	8350296	8350367	E071	29459
chr9	8363574	8363628	E071	42737
chr9	8363887	8363995	E071	43050
chr9	8366881	8366999	E071	46044
chr9	8348714	8348771	E072	27877
chr9	8348801	8348851	E072	27964
chr9	8348907	8349003	E072	28070
chr9	8349230	8349896	E072	28393
chr9	8363887	8363995	E072	43050
chr9	8364076	8364656	E072	43239
chr9	8365067	8365360	E072	44230
chr9	8363887	8363995	E073	43050
chr9	8364076	8364656	E073	43239
chr9	8318454	8318611	E074	-2226
chr9	8348907	8349003	E074	28070
chr9	8349230	8349896	E074	28393
chr9	8363574	8363628	E074	42737
chr9	8363887	8363995	E074	43050
chr9	8365067	8365360	E074	44230
chr9	8289513	8289646	E081	-31191
chr9	8289677	8289748	E081	-31089
chr9	8289770	8289974	E081	-30863
chr9	8318454	8318611	E081	-2226
chr9	8363574	8363628	E081	42737
chr9	8363887	8363995	E081	43050
chr9	8364076	8364656	E081	43239
chr9	8364076	8364656	E082	43239

rs12001948

Genomic Coordinates

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

Population Frequency

P-Value

eQTL of rs12001948 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs12001948 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)