rs2442623

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

MCPH1 : Intron Variant
ANGPT2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0062 (1878/29960,GnomAD)
A=0057 (1676/29118,TOPMED)
A=0044 (221/5008,1000G)
A=0047 (182/3854,ALSPAC)
A=0054 (200/3708,TWINSUK)

Position: chr8:6518817 (GRCh38.p7) (8p23.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 87 Enhancers around

Promoter: 8 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 8	NC_000008.11:g.6518817G>A
GRCh37.p13 chr 8	NC_000008.10:g.6376338G>A
MCPH1 RefSeqGene	NG_016619.2:g.117226G>A
ANGPT2 RefSeqGene	NG_029483.1:g.49447C>T

Gene: ANGPT2, angiopoietin 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ANGPT2 transcript variant 2	NM_001118887.1:c.	N/A	Intron Variant
ANGPT2 transcript variant 3	NM_001118888.1:c.	N/A	Intron Variant
ANGPT2 transcript variant 1	NM_001147.2:c.	N/A	Intron Variant
ANGPT2 transcript variant X1	XM_017013318.1:c.	N/A	Intron Variant

Gene: MCPH1, microcephalin 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MCPH1 transcript variant 4	NM_001322042.1:c.	N/A	Intron Variant
MCPH1 transcript variant 1	NM_024596.4:c.	N/A	Intron Variant
MCPH1 transcript variant 2	NM_001172574.1:c.	N/A	Genic Downstream Transcript Variant
MCPH1 transcript variant 3	NM_001172575.1:c.	N/A	Genic Downstream Transcript Variant
MCPH1 transcript variant 5	NM_001322043.1:c.	N/A	Genic Downstream Transcript Variant
MCPH1 transcript variant 6	NM_001322045.1:c.	N/A	Genic Downstream Transcript Variant
MCPH1 transcript variant 7	NR_136159.1:n.	N/A	Genic Downstream Transcript 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 X11	XM_011534759.2:c.	N/A	Intron Variant
MCPH1 transcript variant X13	XM_011534760.2: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 X10	XM_011534758.2:c.	N/A	Genic Downstream Transcript Variant
MCPH1 transcript variant X4	XR_001745596.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.917	A=0.083
1000Genomes	American	Sub	694	G=0.960	A=0.040
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=0.948	A=0.052
1000Genomes	Global	Study-wide	5008	G=0.956	A=0.044
1000Genomes	South Asian	Sub	978	G=0.970	A=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.953	A=0.047
The Genome Aggregation Database	African	Sub	8720	G=0.921	A=0.079
The Genome Aggregation Database	American	Sub	834	G=0.970	A=0.030
The Genome Aggregation Database	East Asian	Sub	1620	G=0.999	A=0.001
The Genome Aggregation Database	Europe	Sub	18484	G=0.937	A=0.062
The Genome Aggregation Database	Global	Study-wide	29960	G=0.937	A=0.062
The Genome Aggregation Database	Other	Sub	302	G=0.980	A=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.942	A=0.057
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.946	A=0.054

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

SNP ID	p-value	Traits	Study
rs2442623	0.000611	nicotine smoking	19268276

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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	6375135	6375205	E067	-1133
chr8	6375319	6375386	E067	-952
chr8	6376467	6376628	E067	129
chr8	6376739	6376779	E067	401
chr8	6377214	6377299	E067	876
chr8	6377318	6377446	E067	980
chr8	6341910	6342492	E068	-33846
chr8	6372739	6373003	E068	-3335
chr8	6373046	6373114	E068	-3224
chr8	6373289	6373602	E068	-2736
chr8	6377318	6377446	E068	980
chr8	6386037	6386392	E068	9699
chr8	6404169	6405777	E068	27831
chr8	6372222	6372371	E069	-3967
chr8	6372669	6372734	E069	-3604
chr8	6372739	6373003	E069	-3335
chr8	6373046	6373114	E069	-3224
chr8	6373289	6373602	E069	-2736
chr8	6375135	6375205	E069	-1133
chr8	6375319	6375386	E069	-952
chr8	6376467	6376628	E069	129
chr8	6376739	6376779	E069	401
chr8	6377214	6377299	E069	876
chr8	6377318	6377446	E069	980
chr8	6377214	6377299	E070	876
chr8	6377318	6377446	E070	980
chr8	6407482	6408186	E070	31144
chr8	6408230	6408532	E070	31892
chr8	6408593	6408716	E070	32255
chr8	6408777	6408910	E070	32439
chr8	6408963	6409015	E070	32625
chr8	6332606	6332756	E071	-43582
chr8	6332990	6333055	E071	-43283
chr8	6343231	6343480	E071	-32858
chr8	6372669	6372734	E071	-3604
chr8	6372739	6373003	E071	-3335
chr8	6373046	6373114	E071	-3224
chr8	6373289	6373602	E071	-2736
chr8	6373827	6374531	E071	-1807
chr8	6375135	6375205	E071	-1133
chr8	6375319	6375386	E071	-952
chr8	6376467	6376628	E071	129
chr8	6376739	6376779	E071	401
chr8	6377214	6377299	E071	876
chr8	6377318	6377446	E071	980
chr8	6388202	6388252	E071	11864
chr8	6389805	6390471	E071	13467
chr8	6396038	6396092	E071	19700
chr8	6396274	6396324	E071	19936
chr8	6397950	6398087	E071	21612
chr8	6398166	6398494	E071	21828
chr8	6398600	6398745	E071	22262
chr8	6398811	6398903	E071	22473
chr8	6398914	6399114	E071	22576
chr8	6423143	6423193	E071	46805
chr8	6341910	6342492	E072	-33846
chr8	6375135	6375205	E072	-1133
chr8	6375319	6375386	E072	-952
chr8	6376467	6376628	E072	129
chr8	6376739	6376779	E072	401
chr8	6377214	6377299	E072	876
chr8	6377318	6377446	E072	980
chr8	6386037	6386392	E072	9699
chr8	6389126	6389528	E072	12788
chr8	6389558	6389638	E072	13220
chr8	6389805	6390471	E072	13467
chr8	6372669	6372734	E073	-3604
chr8	6372739	6373003	E073	-3335
chr8	6373046	6373114	E073	-3224
chr8	6373289	6373602	E073	-2736
chr8	6377214	6377299	E073	876
chr8	6377318	6377446	E073	980
chr8	6402279	6402397	E073	25941
chr8	6341910	6342492	E074	-33846
chr8	6375135	6375205	E074	-1133
chr8	6375319	6375386	E074	-952
chr8	6376467	6376628	E074	129
chr8	6376739	6376779	E074	401
chr8	6377214	6377299	E074	876
chr8	6377318	6377446	E074	980
chr8	6389126	6389528	E074	12788
chr8	6389558	6389638	E074	13220
chr8	6389805	6390471	E074	13467
chr8	6417819	6419149	E074	41481
chr8	6397950	6398087	E081	21612
chr8	6398166	6398494	E081	21828
chr8	6399918	6399968	E081	23580

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr8	6419361	6421021	E067	43023
chr8	6419361	6421021	E068	43023
chr8	6419361	6421021	E069	43023
chr8	6419361	6421021	E070	43023
chr8	6419361	6421021	E071	43023
chr8	6419361	6421021	E072	43023
chr8	6419361	6421021	E073	43023
chr8	6419361	6421021	E074	43023

rs2442623

Genomic Coordinates

Gene: ANGPT2, angiopoietin 2(minus strand)

Gene: MCPH1, microcephalin 1(plus strand)

Population Frequency

P-Value

eQTL of rs2442623 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs2442623 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)