SNP Detail Info-rs678892

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.55340661G>A
GRCh38.p7 chr 15	NC_000015.10:g.55340661G>C
GRCh38.p7 chr 15	NC_000015.10:g.55340661G>T
GRCh37.p13 chr 15	NC_000015.9:g.55632859G>A
GRCh37.p13 chr 15	NC_000015.9:g.55632859G>C
GRCh37.p13 chr 15	NC_000015.9:g.55632859G>T

Gene: PIGB, phosphatidylinositol glycan anchor biosynthesis class B(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PIGB transcript	NM_004855.4:c.896G>A	W [TGG]> * [TAG]	Coding Sequence Variant
GPI mannosyltransferase 3	NP_004846.4:p.Trp...NP_004846.4:p.Trp299Ter	W [Trp]> * [Ter]	Stop Gained
PIGB transcript	NM_004855.4:c.896G>C	W [TGG]> S [TCG]	Coding Sequence Variant
GPI mannosyltransferase 3	NP_004846.4:p.Trp...NP_004846.4:p.Trp299Ser	W [Trp]> S [Ser]	Missense Variant
PIGB transcript	NM_004855.4:c.896G>T	W [TGG]> L [TTG]	Coding Sequence Variant
GPI mannosyltransferase 3	NP_004846.4:p.Trp...NP_004846.4:p.Trp299Leu	W [Trp]> L [Leu]	Missense Variant
PIGB transcript variant X1	XM_011522235.2:c....XM_011522235.2:c.851G>A	W [TGG]> * [TAG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X1	XP_011520537.1:p....XP_011520537.1:p.Trp284Ter	W [Trp]> * [Ter]	Stop Gained
PIGB transcript variant X1	XM_011522235.2:c....XM_011522235.2:c.851G>C	W [TGG]> S [TCG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X1	XP_011520537.1:p....XP_011520537.1:p.Trp284Ser	W [Trp]> S [Ser]	Missense Variant
PIGB transcript variant X1	XM_011522235.2:c....XM_011522235.2:c.851G>T	W [TGG]> L [TTG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X1	XP_011520537.1:p....XP_011520537.1:p.Trp284Leu	W [Trp]> L [Leu]	Missense Variant
PIGB transcript variant X2	XM_011522236.2:c....XM_011522236.2:c.791G>A	W [TGG]> * [TAG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X2	XP_011520538.1:p....XP_011520538.1:p.Trp264Ter	W [Trp]> * [Ter]	Stop Gained
PIGB transcript variant X2	XM_011522236.2:c....XM_011522236.2:c.791G>C	W [TGG]> S [TCG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X2	XP_011520538.1:p....XP_011520538.1:p.Trp264Ser	W [Trp]> S [Ser]	Missense Variant
PIGB transcript variant X2	XM_011522236.2:c....XM_011522236.2:c.791G>T	W [TGG]> L [TTG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X2	XP_011520538.1:p....XP_011520538.1:p.Trp264Leu	W [Trp]> L [Leu]	Missense Variant
PIGB transcript variant X3	XM_017022730.1:c....XM_017022730.1:c.497G>A	W [TGG]> * [TAG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X3	XP_016878219.1:p....XP_016878219.1:p.Trp166Ter	W [Trp]> * [Ter]	Stop Gained
PIGB transcript variant X3	XM_017022730.1:c....XM_017022730.1:c.497G>C	W [TGG]> S [TCG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X3	XP_016878219.1:p....XP_016878219.1:p.Trp166Ser	W [Trp]> S [Ser]	Missense Variant
PIGB transcript variant X3	XM_017022730.1:c....XM_017022730.1:c.497G>T	W [TGG]> L [TTG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X3	XP_016878219.1:p....XP_016878219.1:p.Trp166Leu	W [Trp]> L [Leu]	Missense Variant
PIGB transcript variant X4	XM_017022731.1:c....XM_017022731.1:c.497G>A	W [TGG]> * [TAG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X3	XP_016878220.1:p....XP_016878220.1:p.Trp166Ter	W [Trp]> * [Ter]	Stop Gained
PIGB transcript variant X4	XM_017022731.1:c....XM_017022731.1:c.497G>C	W [TGG]> S [TCG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X3	XP_016878220.1:p....XP_016878220.1:p.Trp166Ser	W [Trp]> S [Ser]	Missense Variant
PIGB transcript variant X4	XM_017022731.1:c....XM_017022731.1:c.497G>T	W [TGG]> L [TTG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X3	XP_016878220.1:p....XP_016878220.1:p.Trp166Leu	W [Trp]> L [Leu]	Missense Variant
PIGB transcript variant X5	XM_011522237.2:c....XM_011522237.2:c.497G>A	W [TGG]> * [TAG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X3	XP_011520539.1:p....XP_011520539.1:p.Trp166Ter	W [Trp]> * [Ter]	Stop Gained
PIGB transcript variant X5	XM_011522237.2:c....XM_011522237.2:c.497G>C	W [TGG]> S [TCG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X3	XP_011520539.1:p....XP_011520539.1:p.Trp166Ser	W [Trp]> S [Ser]	Missense Variant
PIGB transcript variant X5	XM_011522237.2:c....XM_011522237.2:c.497G>T	W [TGG]> L [TTG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X3	XP_011520539.1:p....XP_011520539.1:p.Trp166Leu	W [Trp]> L [Leu]	Missense Variant
PIGB transcript variant X7	XM_005254795.4:c....XM_005254795.4:c.413G>A	W [TGG]> * [TAG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X4	XP_005254852.1:p....XP_005254852.1:p.Trp138Ter	W [Trp]> * [Ter]	Stop Gained
PIGB transcript variant X7	XM_005254795.4:c....XM_005254795.4:c.413G>C	W [TGG]> S [TCG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X4	XP_005254852.1:p....XP_005254852.1:p.Trp138Ser	W [Trp]> S [Ser]	Missense Variant
PIGB transcript variant X7	XM_005254795.4:c....XM_005254795.4:c.413G>T	W [TGG]> L [TTG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X4	XP_005254852.1:p....XP_005254852.1:p.Trp138Leu	W [Trp]> L [Leu]	Missense Variant
PIGB transcript variant X9	XM_017022732.1:c....XM_017022732.1:c.368G>A	W [TGG]> * [TAG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X5	XP_016878221.1:p....XP_016878221.1:p.Trp123Ter	W [Trp]> * [Ter]	Stop Gained
PIGB transcript variant X9	XM_017022732.1:c....XM_017022732.1:c.368G>C	W [TGG]> S [TCG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X5	XP_016878221.1:p....XP_016878221.1:p.Trp123Ser	W [Trp]> S [Ser]	Missense Variant
PIGB transcript variant X9	XM_017022732.1:c....XM_017022732.1:c.368G>T	W [TGG]> L [TTG]	Coding Sequence Variant
GPI mannosyltransferase 3 isoform X5	XP_016878221.1:p....XP_016878221.1:p.Trp123Leu	W [Trp]> L [Leu]	Missense Variant
PIGB transcript variant X6	XR_001751422.1:n....XR_001751422.1:n.1212G>A	G>A	Non Coding Transcript Variant
PIGB transcript variant X6	XR_001751422.1:n....XR_001751422.1:n.1212G>C	G>C	Non Coding Transcript Variant
PIGB transcript variant X6	XR_001751422.1:n....XR_001751422.1:n.1212G>T	G>T	Non Coding Transcript Variant
PIGB transcript variant X8	XR_931950.2:n.121...XR_931950.2:n.1212G>A	G>A	Non Coding Transcript Variant
PIGB transcript variant X8	XR_931950.2:n.121...XR_931950.2:n.1212G>C	G>C	Non Coding Transcript Variant
PIGB transcript variant X8	XR_931950.2:n.121...XR_931950.2:n.1212G>T	G>T	Non Coding Transcript Variant
PIGB transcript variant X10	XR_001751423.1:n....XR_001751423.1:n.1167G>A	G>A	Non Coding Transcript Variant
PIGB transcript variant X10	XR_001751423.1:n....XR_001751423.1:n.1167G>C	G>C	Non Coding Transcript Variant
PIGB transcript variant X10	XR_001751423.1:n....XR_001751423.1:n.1167G>T	G>T	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.112	T=0.888
1000Genomes	American	Sub	694	G=0.590	T=0.410
1000Genomes	East Asian	Sub	1008	G=0.236	T=0.764
1000Genomes	Europe	Sub	1006	G=0.652	T=0.348
1000Genomes	Global	Study-wide	5008	G=0.399	T=0.601
1000Genomes	South Asian	Sub	978	G=0.560	T=0.440
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.665	T=0.335
The Exome Aggregation Consortium	American	Sub	20216	G=0.391	T=0.608
The Exome Aggregation Consortium	Asian	Sub	23768	G=0.457	T=0.542
The Exome Aggregation Consortium	Europe	Sub	68318	G=0.673	T=0.326
The Exome Aggregation Consortium	Global	Study-wide	113158	G=0.577	T=0.422
The Exome Aggregation Consortium	Other	Sub	856	G=0.610	T=0.390
The Genome Aggregation Database	African	Sub	8696	G=0.203	T=0.797
The Genome Aggregation Database	American	Sub	832	G=0.540	T=0.460
The Genome Aggregation Database	East Asian	Sub	1608	G=0.228	T=0.772
The Genome Aggregation Database	Europe	Sub	18438	G=0.683	T=0.316
The Genome Aggregation Database	Global	Study-wide	29876	G=0.515	T=0.484
The Genome Aggregation Database	Other	Sub	302	G=0.660	T=0.340
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.449	T=0.550
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.662	T=0.338

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
rs678892	0.000232	cocaine dependence	23958962
rs678892	0.000245	cocaine dependence	23958962

eQTL of rs678892 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr15:55632859	PIGB	ENSG00000069943.5	G>T	1.7726e-4	21499	Frontal_Cortex_BA9
Chr15:55632859	PIGB	ENSG00000069943.5	G>T	3.2645e-3	21499	Brain_Spinal_cord_cervical

meQTL of rs678892 in Fetal Brain

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

rs678892

Genomic Coordinates

Gene: PIGB, phosphatidylinositol glycan anchor biosynthesis class B(plus strand)

Population Frequency

P-Value

eQTL of rs678892 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs678892 in Fetal Brain

Genomic View

Chromatin Interaction