SNP Detail Info-rs13031275

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.151489980A>C
GRCh37.p13 chr 2	NC_000002.11:g.152346494A>C
NEB RefSeqGene	LRG_202

Gene: RIF1, replication timing regulatory factor 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RIF1 transcript variant 2	NM_001177663.1:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant 3	NM_001177664.1:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant 4	NM_001177665.1:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant 1	NM_018151.4:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant X1	XM_005246665.3:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant X13	XM_011511395.2:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant X10	XM_017004422.1:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant X11	XM_017004423.1:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant X12	XM_017004424.1:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant X12	XM_017004425.1:c.	N/A	Genic Downstream Transcript Variant
RIF1 transcript variant X2	XR_001738811.1:n.	N/A	Intron Variant
RIF1 transcript variant X3	XR_001738812.1:n.	N/A	Intron Variant
RIF1 transcript variant X4	XR_001738813.1:n.	N/A	Intron Variant
RIF1 transcript variant X5	XR_001738814.1:n.	N/A	Intron Variant
RIF1 transcript variant X6	XR_001738815.1:n.	N/A	Intron Variant
RIF1 transcript variant X7	XR_001738816.1:n.	N/A	Intron Variant
RIF1 transcript variant X8	XR_001738817.1:n.	N/A	Intron Variant

Gene: NEB, nebulin(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NEB transcript variant 1	NM_001164507.1:c....NM_001164507.1:c.25395T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform 1	NP_001157979.1:p....NP_001157979.1:p.Ser8465=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant 2	NM_001164508.1:c....NM_001164508.1:c.25395T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform 2	NP_001157980.1:p....NP_001157980.1:p.Ser8465=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant 3	NM_004543.4:c.198...NM_004543.4:c.19827T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform 3	NP_004534.2:p.Ser...NP_004534.2:p.Ser6609=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant 4	NM_001271208.1:c....NM_001271208.1:c.25500T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform 4	NP_001258137.1:p....NP_001258137.1:p.Ser8500=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X33	XM_005246616.1:c.	N/A	Genic Downstream Transcript Variant
NEB transcript variant X1	XM_005246590.2:c....XM_005246590.2:c.25302T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X1	XP_005246647.1:p....XP_005246647.1:p.Ser8434=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X2	XM_005246591.2:c....XM_005246591.2:c.25302T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X2	XP_005246648.1:p....XP_005246648.1:p.Ser8434=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X3	XM_005246593.2:c....XM_005246593.2:c.25302T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X3	XP_005246650.1:p....XP_005246650.1:p.Ser8434=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X4	XM_005246594.2:c....XM_005246594.2:c.25302T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X4	XP_005246651.1:p....XP_005246651.1:p.Ser8434=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X5	XM_005246592.2:c....XM_005246592.2:c.25302T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X5	XP_005246649.1:p....XP_005246649.1:p.Ser8434=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X6	XM_017004177.1:c....XM_017004177.1:c.25284T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X6	XP_016859666.1:p....XP_016859666.1:p.Ser8428=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X7	XM_005246596.2:c....XM_005246596.2:c.25209T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X7	XP_005246653.1:p....XP_005246653.1:p.Ser8403=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X8	XM_017004178.1:c....XM_017004178.1:c.25209T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X8	XP_016859667.1:p....XP_016859667.1:p.Ser8403=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X9	XM_005246597.2:c....XM_005246597.2:c.25209T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X9	XP_005246654.1:p....XP_005246654.1:p.Ser8403=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X10	XM_005246598.2:c....XM_005246598.2:c.25209T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X10	XP_005246655.1:p....XP_005246655.1:p.Ser8403=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X11	XM_005246599.2:c....XM_005246599.2:c.25116T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X11	XP_005246656.1:p....XP_005246656.1:p.Ser8372=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X12	XM_005246600.2:c....XM_005246600.2:c.25116T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X12	XP_005246657.1:p....XP_005246657.1:p.Ser8372=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X12	XM_005246601.2:c....XM_005246601.2:c.25023T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X12	XP_005246658.1:p....XP_005246658.1:p.Ser8341=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X13	XM_005246602.2:c....XM_005246602.2:c.25023T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X13	XP_005246659.1:p....XP_005246659.1:p.Ser8341=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X14	XM_005246603.2:c....XM_005246603.2:c.24930T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X14	XP_005246660.1:p....XP_005246660.1:p.Ser8310=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X15	XM_005246604.2:c....XM_005246604.2:c.24930T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X15	XP_005246661.1:p....XP_005246661.1:p.Ser8310=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X16	XM_017004179.1:c....XM_017004179.1:c.24930T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X16	XP_016859668.1:p....XP_016859668.1:p.Ser8310=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X17	XM_006712541.2:c....XM_006712541.2:c.24930T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X17	XP_006712604.1:p....XP_006712604.1:p.Ser8310=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X18	XM_005246606.2:c....XM_005246606.2:c.24930T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X18	XP_005246663.1:p....XP_005246663.1:p.Ser8310=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X19	XM_017004180.1:c....XM_017004180.1:c.24930T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X19	XP_016859669.1:p....XP_016859669.1:p.Ser8310=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X20	XM_006712542.2:c....XM_006712542.2:c.24930T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X20	XP_006712605.1:p....XP_006712605.1:p.Ser8310=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X21	XM_017004181.1:c....XM_017004181.1:c.24837T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X21	XP_016859670.1:p....XP_016859670.1:p.Ser8279=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X22	XM_005246608.2:c....XM_005246608.2:c.24837T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X22	XP_005246665.1:p....XP_005246665.1:p.Ser8279=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X23	XM_017004182.1:c....XM_017004182.1:c.24744T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X23	XP_016859671.1:p....XP_016859671.1:p.Ser8248=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X24	XM_005246610.2:c....XM_005246610.2:c.24744T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X24	XP_005246667.1:p....XP_005246667.1:p.Ser8248=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X25	XM_005246611.2:c....XM_005246611.2:c.24744T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X25	XP_005246668.1:p....XP_005246668.1:p.Ser8248=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X26	XM_005246612.2:c....XM_005246612.2:c.24666T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X26	XP_005246669.1:p....XP_005246669.1:p.Ser8222=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X27	XM_005246613.2:c....XM_005246613.2:c.24666T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X27	XP_005246670.1:p....XP_005246670.1:p.Ser8222=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X28	XM_017004183.1:c....XM_017004183.1:c.24651T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X28	XP_016859672.1:p....XP_016859672.1:p.Ser8217=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X29	XM_011511225.2:c....XM_011511225.2:c.24651T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X29	XP_011509527.1:p....XP_011509527.1:p.Ser8217=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X30	XM_017004184.1:c....XM_017004184.1:c.24651T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X30	XP_016859673.1:p....XP_016859673.1:p.Ser8217=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X31	XM_005246615.2:c....XM_005246615.2:c.24651T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X31	XP_005246672.1:p....XP_005246672.1:p.Ser8217=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X32	XM_017004185.1:c....XM_017004185.1:c.24372T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X32	XP_016859674.1:p....XP_016859674.1:p.Ser8124=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X34	XM_011511226.2:c....XM_011511226.2:c.23208T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X34	XP_011509528.1:p....XP_011509528.1:p.Ser7736=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X35	XM_005246617.2:c....XM_005246617.2:c.22479T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X35	XP_005246674.1:p....XP_005246674.1:p.Ser7493=	S [Ser]> S [Ser]	Synonymous Variant
NEB transcript variant X36	XM_011511227.2:c....XM_011511227.2:c.21021T>G	S [TCT]> S [TCG]	Coding Sequence Variant
nebulin isoform X36	XP_011509529.1:p....XP_011509529.1:p.Ser7007=	S [Ser]> S [Ser]	Synonymous Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.996	C=0.004
1000Genomes	American	Sub	694	A=0.970	C=0.030
1000Genomes	East Asian	Sub	1008	A=1.000	C=0.000
1000Genomes	Europe	Sub	1006	A=0.953	C=0.047
1000Genomes	Global	Study-wide	5008	A=0.983	C=0.017
1000Genomes	South Asian	Sub	978	A=0.990	C=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.932	C=0.068
The Exome Aggregation Consortium	American	Sub	21376	A=0.983	C=0.017
The Exome Aggregation Consortium	Asian	Sub	25128	A=0.985	C=0.014
The Exome Aggregation Consortium	Europe	Sub	73352	A=0.937	C=0.062
The Exome Aggregation Consortium	Global	Study-wide	120754	A=0.955	C=0.044
The Exome Aggregation Consortium	Other	Sub	898	A=0.970	C=0.030
The Genome Aggregation Database	African	Sub	8728	A=0.988	C=0.012
The Genome Aggregation Database	American	Sub	838	A=0.980	C=0.020
The Genome Aggregation Database	East Asian	Sub	1620	A=1.000	C=0.000
The Genome Aggregation Database	Europe	Sub	18488	A=0.947	C=0.052
The Genome Aggregation Database	Global	Study-wide	29976	A=0.963	C=0.036
The Genome Aggregation Database	Other	Sub	302	A=0.950	C=0.050
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.962	C=0.037
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.937	C=0.063

PMID	Title	Author	Journal
29071344	Genetic Risk Variants Associated With Comorbid Alcohol Dependence and Major Depression.	Zhou H	JAMA Psychiatry
24033266	A systematic approach to assessing the clinical significance of genetic variants.	Duzkale H	Clin Genet
25741868	Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.	Richards S	Genet Med

P-Value

SNP ID	p-value	Traits	Study
rs13031275	5E-06	alcohol dependence	29071344

eQTL of rs13031275 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 rs13031275 in Fetal Brain

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	152297234	152297305	E067	-49189
chr2	152297234	152297305	E068	-49189
chr2	152297234	152297305	E071	-49189

rs13031275

Genomic Coordinates

Gene: RIF1, replication timing regulatory factor 1(plus strand)

Gene: NEB, nebulin(minus strand)

Population Frequency

P-Value

eQTL of rs13031275 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs13031275 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)