rs7018378

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

MCPH1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0185 (5549/29944,GnomAD)
A=0180 (5242/29118,TOPMED)
A=0114 (572/5008,1000G)
A=0248 (957/3854,ALSPAC)
A=0244 (905/3708,TWINSUK)

Position: chr8:6420991 (GRCh38.p7) (8p23.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 97 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 8	NC_000008.11:g.6420991G>A
GRCh37.p13 chr 8	NC_000008.10:g.6278512G>A
MCPH1 RefSeqGene	NG_016619.2:g.19400G>A

Gene: MCPH1, microcephalin 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MCPH1 transcript variant 2	NM_001172574.1:c.	N/A	Intron Variant
MCPH1 transcript variant 3	NM_001172575.1:c.	N/A	Intron Variant
MCPH1 transcript variant 4	NM_001322042.1:c.	N/A	Intron Variant
MCPH1 transcript variant 5	NM_001322043.1:c.	N/A	Intron Variant
MCPH1 transcript variant 6	NM_001322045.1:c.	N/A	Intron Variant
MCPH1 transcript variant 1	NM_024596.4:c.	N/A	Intron Variant
MCPH1 transcript variant 7	NR_136159.1:n.	N/A	Intron Variant
MCPH1 transcript variant X2	XM_011534755.2:c.	N/A	Intron Variant
MCPH1 transcript variant X7	XM_011534756.2:c.	N/A	Intron Variant
MCPH1 transcript variant X8	XM_011534757.2:c.	N/A	Intron Variant
MCPH1 transcript variant X10	XM_011534758.2:c.	N/A	Intron Variant
MCPH1 transcript variant X11	XM_011534759.2:c.	N/A	Intron Variant
MCPH1 transcript variant X1	XM_017013829.1:c.	N/A	Intron Variant
MCPH1 transcript variant X3	XM_017013830.1:c.	N/A	Intron Variant
MCPH1 transcript variant X5	XM_017013831.1:c.	N/A	Intron Variant
MCPH1 transcript variant X6	XM_017013832.1:c.	N/A	Intron Variant
MCPH1 transcript variant X9	XM_017013833.1:c.	N/A	Intron Variant
MCPH1 transcript variant X12	XM_017013834.1:c.	N/A	Intron Variant
MCPH1 transcript variant X13	XM_011534760.2:c.	N/A	Genic Upstream Transcript Variant
MCPH1 transcript variant X4	XR_001745596.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.927	A=0.073
1000Genomes	American	Sub	694	G=0.840	A=0.160
1000Genomes	East Asian	Sub	1008	G=0.971	A=0.029
1000Genomes	Europe	Sub	1006	G=0.740	A=0.260
1000Genomes	Global	Study-wide	5008	G=0.886	A=0.114
1000Genomes	South Asian	Sub	978	G=0.920	A=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.752	A=0.248
The Genome Aggregation Database	African	Sub	8708	G=0.892	A=0.108
The Genome Aggregation Database	American	Sub	836	G=0.850	A=0.150
The Genome Aggregation Database	East Asian	Sub	1622	G=0.990	A=0.010
The Genome Aggregation Database	Europe	Sub	18476	G=0.763	A=0.236
The Genome Aggregation Database	Global	Study-wide	29944	G=0.814	A=0.185
The Genome Aggregation Database	Other	Sub	302	G=0.680	A=0.320
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.820	A=0.180
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.756	A=0.244

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs7018378	3.95E-05	nicotine smoking	19268276

eQTL of rs7018378 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 rs7018378 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 )
chr8	6273755	6274130	E067	-4382
chr8	6282206	6282462	E067	3694
chr8	6282473	6283575	E067	3961
chr8	6285821	6286738	E067	7309
chr8	6286791	6287068	E067	8279
chr8	6287283	6287333	E067	8771
chr8	6287426	6287515	E067	8914
chr8	6287523	6287675	E067	9011
chr8	6282473	6283575	E068	3961
chr8	6286791	6287068	E068	8279
chr8	6287283	6287333	E068	8771
chr8	6287426	6287515	E068	8914
chr8	6287523	6287675	E068	9011
chr8	6292417	6293208	E068	13905
chr8	6321109	6321197	E068	42597
chr8	6321232	6321942	E068	42720
chr8	6262492	6262631	E069	-15881
chr8	6282206	6282462	E069	3694
chr8	6282473	6283575	E069	3961
chr8	6286791	6287068	E069	8279
chr8	6287283	6287333	E069	8771
chr8	6287426	6287515	E069	8914
chr8	6287523	6287675	E069	9011
chr8	6320630	6320690	E069	42118
chr8	6320735	6321027	E069	42223
chr8	6321109	6321197	E069	42597
chr8	6321232	6321942	E069	42720
chr8	6267271	6267325	E070	-11187
chr8	6321232	6321942	E070	42720
chr8	6322011	6322077	E070	43499
chr8	6322436	6322499	E070	43924
chr8	6322627	6322782	E070	44115
chr8	6262648	6262914	E071	-15598
chr8	6281308	6282158	E071	2796
chr8	6282206	6282462	E071	3694
chr8	6282473	6283575	E071	3961
chr8	6285821	6286738	E071	7309
chr8	6286791	6287068	E071	8279
chr8	6287283	6287333	E071	8771
chr8	6287426	6287515	E071	8914
chr8	6287523	6287675	E071	9011
chr8	6292417	6293208	E071	13905
chr8	6317288	6317357	E071	38776
chr8	6320630	6320690	E071	42118
chr8	6320735	6321027	E071	42223
chr8	6321109	6321197	E071	42597
chr8	6321232	6321942	E071	42720
chr8	6322011	6322077	E071	43499
chr8	6265413	6265467	E072	-13045
chr8	6265524	6265564	E072	-12948
chr8	6282206	6282462	E072	3694
chr8	6282473	6283575	E072	3961
chr8	6285821	6286738	E072	7309
chr8	6286791	6287068	E072	8279
chr8	6287283	6287333	E072	8771
chr8	6287426	6287515	E072	8914
chr8	6287523	6287675	E072	9011
chr8	6320630	6320690	E072	42118
chr8	6320735	6321027	E072	42223
chr8	6321109	6321197	E072	42597
chr8	6321232	6321942	E072	42720
chr8	6262648	6262914	E073	-15598
chr8	6282206	6282462	E073	3694
chr8	6282473	6283575	E073	3961
chr8	6286791	6287068	E073	8279
chr8	6287283	6287333	E073	8771
chr8	6287426	6287515	E073	8914
chr8	6287523	6287675	E073	9011
chr8	6321109	6321197	E073	42597
chr8	6321232	6321942	E073	42720
chr8	6322011	6322077	E073	43499
chr8	6273755	6274130	E074	-4382
chr8	6281308	6282158	E074	2796
chr8	6282206	6282462	E074	3694
chr8	6282473	6283575	E074	3961
chr8	6285821	6286738	E074	7309
chr8	6286791	6287068	E074	8279
chr8	6287283	6287333	E074	8771
chr8	6287426	6287515	E074	8914
chr8	6287523	6287675	E074	9011
chr8	6317288	6317357	E074	38776
chr8	6320021	6320080	E074	41509
chr8	6320270	6320310	E074	41758
chr8	6320427	6320528	E074	41915
chr8	6320630	6320690	E074	42118
chr8	6320735	6321027	E074	42223
chr8	6321109	6321197	E074	42597
chr8	6321232	6321942	E074	42720
chr8	6262648	6262914	E081	-15598
chr8	6265413	6265467	E081	-13045
chr8	6265524	6265564	E081	-12948
chr8	6286791	6287068	E081	8279
chr8	6262492	6262631	E082	-15881
chr8	6262648	6262914	E082	-15598
chr8	6265413	6265467	E082	-13045
chr8	6265524	6265564	E082	-12948
chr8	6267271	6267325	E082	-11187

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr8	6263022	6265124	E067	-13388
chr8	6263022	6265124	E068	-13388
chr8	6263022	6265124	E069	-13388
chr8	6263022	6265124	E070	-13388
chr8	6263022	6265124	E071	-13388
chr8	6263022	6265124	E072	-13388
chr8	6263022	6265124	E073	-13388
chr8	6263022	6265124	E074	-13388
chr8	6263022	6265124	E081	-13388
chr8	6263022	6265124	E082	-13388