rs10864540

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

C1orf167 : Intron Variant
LOC102724659 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0318 (9451/29646,GnomAD)
A==0361 (10536/29118,TOPMED)
A==0299 (1499/5008,1000G)
A==0279 (1075/3854,ALSPAC)
A==0287 (1064/3708,TWINSUK)

Position: chr1:11778042 (GRCh38.p7) (1p36.22)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 141 Enhancers around

Promoter: 21 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.11778042A>G
GRCh37.p13 chr 1	NC_000001.10:g.11838099A>G

Gene: C1orf167, chromosome 1 open reading frame 167(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C1orf167 transcript	NM_001010881.1:c.	N/A	Intron Variant
C1orf167 transcript variant X3	XM_011541269.2:c.	N/A	Intron Variant
C1orf167 transcript variant X5	XM_011541271.2:c.	N/A	Intron Variant
C1orf167 transcript variant X1	XM_011541272.2:c.	N/A	Intron Variant
C1orf167 transcript variant X7	XM_011541274.2:c.	N/A	Intron Variant
C1orf167 transcript variant X8	XM_011541275.2:c.	N/A	Intron Variant
C1orf167 transcript variant X6	XM_011541276.2:c.	N/A	Intron Variant
C1orf167 transcript variant X9	XM_011541277.2:c.	N/A	Intron Variant
C1orf167 transcript variant X12	XM_011541278.2:c.	N/A	Intron Variant
C1orf167 transcript variant X12	XM_011541280.2:c.	N/A	Intron Variant
C1orf167 transcript variant X13	XM_011541281.2:c.	N/A	Intron Variant
C1orf167 transcript variant X2	XM_017001062.1:c.	N/A	Intron Variant
C1orf167 transcript variant X4	XM_017001063.1:c.	N/A	Intron Variant
C1orf167 transcript variant X11	XM_017001064.1:c.	N/A	Intron Variant

Gene: LOC102724659, uncharacterized LOC102724659(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102724659 transcript	NR_126000.1:n.903T>C	T>C	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.480	G=0.520
1000Genomes	American	Sub	694	A=0.180	G=0.820
1000Genomes	East Asian	Sub	1008	A=0.116	G=0.884
1000Genomes	Europe	Sub	1006	A=0.271	G=0.729
1000Genomes	Global	Study-wide	5008	A=0.299	G=0.701
1000Genomes	South Asian	Sub	978	A=0.350	G=0.650
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.279	G=0.721
The Genome Aggregation Database	African	Sub	8666	A=0.477	G=0.523
The Genome Aggregation Database	American	Sub	834	A=0.180	G=0.820
The Genome Aggregation Database	East Asian	Sub	1614	A=0.120	G=0.880
The Genome Aggregation Database	Europe	Sub	18230	A=0.266	G=0.733
The Genome Aggregation Database	Global	Study-wide	29646	A=0.318	G=0.681
The Genome Aggregation Database	Other	Sub	302	A=0.350	G=0.650
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.361	G=0.638
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.287	G=0.713

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs10864540	1.72E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs10864540 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:11838099	NPPA-AS1	ENSG00000242349.1	A>G	1.7091e-19	-65662	Cerebellum
Chr1:11838099	NPPA-AS1	ENSG00000242349.1	A>G	4.1732e-12	-65662	Frontal_Cortex_BA9
Chr1:11838099	NPPA-AS1	ENSG00000242349.1	A>G	1.7046e-15	-65662	Hypothalamus
Chr1:11838099	NPPA-AS1	ENSG00000242349.1	A>G	3.4850e-10	-65662	Cortex
Chr1:11838099	NPPA-AS1	ENSG00000242349.1	A>G	1.0946e-15	-65662	Cerebellar_Hemisphere

meQTL of rs10864540 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg21864959	chr1:11847863	MTHFR	-0.072778970258149	2.6544e-17

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 )
chr1	11790101	11790260	E067	-47839
chr1	11792757	11792910	E067	-45189
chr1	11793408	11793462	E067	-44637
chr1	11793527	11793611	E067	-44488
chr1	11795364	11795560	E067	-42539
chr1	11844583	11844653	E067	6484
chr1	11844696	11844804	E067	6597
chr1	11849763	11850278	E067	11664
chr1	11850321	11851442	E067	12222
chr1	11851478	11851738	E067	13379
chr1	11851805	11851986	E067	13706
chr1	11868133	11868248	E067	30034
chr1	11868348	11868426	E067	30249
chr1	11789516	11789711	E068	-48388
chr1	11789718	11790058	E068	-48041
chr1	11792757	11792910	E068	-45189
chr1	11795364	11795560	E068	-42539
chr1	11844583	11844653	E068	6484
chr1	11844696	11844804	E068	6597
chr1	11845987	11846049	E068	7888
chr1	11846304	11846415	E068	8205
chr1	11847219	11847965	E068	9120
chr1	11847998	11848864	E068	9899
chr1	11849763	11850278	E068	11664
chr1	11850321	11851442	E068	12222
chr1	11851478	11851738	E068	13379
chr1	11851805	11851986	E068	13706
chr1	11852198	11852353	E068	14099
chr1	11790101	11790260	E069	-47839
chr1	11790375	11790991	E069	-47108
chr1	11792757	11792910	E069	-45189
chr1	11793408	11793462	E069	-44637
chr1	11793527	11793611	E069	-44488
chr1	11795364	11795560	E069	-42539
chr1	11798161	11798239	E069	-39860
chr1	11798295	11798381	E069	-39718
chr1	11798472	11798551	E069	-39548
chr1	11806872	11806993	E069	-31106
chr1	11807222	11807448	E069	-30651
chr1	11809261	11809507	E069	-28592
chr1	11844479	11844531	E069	6380
chr1	11844583	11844653	E069	6484
chr1	11846770	11847208	E069	8671
chr1	11847219	11847965	E069	9120
chr1	11847998	11848864	E069	9899
chr1	11849763	11850278	E069	11664
chr1	11850321	11851442	E069	12222
chr1	11792757	11792910	E070	-45189
chr1	11847219	11847965	E070	9120
chr1	11868133	11868248	E070	30034
chr1	11868348	11868426	E070	30249
chr1	11869396	11869446	E070	31297
chr1	11789516	11789711	E071	-48388
chr1	11789718	11790058	E071	-48041
chr1	11790101	11790260	E071	-47839
chr1	11792757	11792910	E071	-45189
chr1	11793408	11793462	E071	-44637
chr1	11793527	11793611	E071	-44488
chr1	11795364	11795560	E071	-42539
chr1	11798161	11798239	E071	-39860
chr1	11798295	11798381	E071	-39718
chr1	11807222	11807448	E071	-30651
chr1	11844583	11844653	E071	6484
chr1	11844696	11844804	E071	6597
chr1	11845987	11846049	E071	7888
chr1	11846304	11846415	E071	8205
chr1	11846770	11847208	E071	8671
chr1	11847219	11847965	E071	9120
chr1	11847998	11848864	E071	9899
chr1	11848963	11849180	E071	10864
chr1	11849222	11849272	E071	11123
chr1	11849303	11849745	E071	11204
chr1	11849763	11850278	E071	11664
chr1	11850321	11851442	E071	12222
chr1	11851478	11851738	E071	13379
chr1	11851805	11851986	E071	13706
chr1	11852198	11852353	E071	14099
chr1	11868133	11868248	E071	30034
chr1	11868348	11868426	E071	30249
chr1	11789516	11789711	E072	-48388
chr1	11789718	11790058	E072	-48041
chr1	11790101	11790260	E072	-47839
chr1	11790375	11790991	E072	-47108
chr1	11792757	11792910	E072	-45189
chr1	11793408	11793462	E072	-44637
chr1	11793527	11793611	E072	-44488
chr1	11795364	11795560	E072	-42539
chr1	11807222	11807448	E072	-30651
chr1	11809261	11809507	E072	-28592
chr1	11844583	11844653	E072	6484
chr1	11844696	11844804	E072	6597
chr1	11846770	11847208	E072	8671
chr1	11847219	11847965	E072	9120
chr1	11849763	11850278	E072	11664
chr1	11850321	11851442	E072	12222
chr1	11851478	11851738	E072	13379
chr1	11868133	11868248	E072	30034
chr1	11868348	11868426	E072	30249
chr1	11869396	11869446	E072	31297
chr1	11790101	11790260	E073	-47839
chr1	11790375	11790991	E073	-47108
chr1	11792757	11792910	E073	-45189
chr1	11795364	11795560	E073	-42539
chr1	11812633	11812709	E073	-25390
chr1	11844479	11844531	E073	6380
chr1	11844583	11844653	E073	6484
chr1	11844696	11844804	E073	6597
chr1	11847219	11847965	E073	9120
chr1	11847998	11848864	E073	9899
chr1	11849763	11850278	E073	11664
chr1	11850321	11851442	E073	12222
chr1	11851478	11851738	E073	13379
chr1	11869396	11869446	E073	31297
chr1	11789516	11789711	E074	-48388
chr1	11789718	11790058	E074	-48041
chr1	11790101	11790260	E074	-47839
chr1	11790375	11790991	E074	-47108
chr1	11792757	11792910	E074	-45189
chr1	11795364	11795560	E074	-42539
chr1	11798800	11798905	E074	-39194
chr1	11798971	11799135	E074	-38964
chr1	11806872	11806993	E074	-31106
chr1	11807222	11807448	E074	-30651
chr1	11844696	11844804	E074	6597
chr1	11847219	11847965	E074	9120
chr1	11847998	11848864	E074	9899
chr1	11848963	11849180	E074	10864
chr1	11849222	11849272	E074	11123
chr1	11849303	11849745	E074	11204
chr1	11849763	11850278	E074	11664
chr1	11850321	11851442	E074	12222
chr1	11851478	11851738	E074	13379
chr1	11851805	11851986	E074	13706
chr1	11790375	11790991	E081	-47108
chr1	11844583	11844653	E081	6484
chr1	11844696	11844804	E081	6597
chr1	11868133	11868248	E081	30034
chr1	11868348	11868426	E081	30249
chr1	11869396	11869446	E081	31297
chr1	11868133	11868248	E082	30034
chr1	11868348	11868426	E082	30249

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	11795591	11798039	E067	-40060
chr1	11864535	11867082	E067	26436
chr1	11795591	11798039	E068	-40060
chr1	11864535	11867082	E068	26436
chr1	11795591	11798039	E069	-40060
chr1	11862034	11862095	E069	23935
chr1	11864535	11867082	E069	26436
chr1	11795591	11798039	E070	-40060
chr1	11864535	11867082	E070	26436
chr1	11795591	11798039	E071	-40060
chr1	11864535	11867082	E071	26436
chr1	11795591	11798039	E072	-40060
chr1	11864535	11867082	E072	26436
chr1	11864535	11867082	E073	26436
chr1	11795591	11798039	E074	-40060
chr1	11864535	11867082	E074	26436
chr1	11795591	11798039	E081	-40060
chr1	11862034	11862095	E081	23935
chr1	11864535	11867082	E081	26436
chr1	11795591	11798039	E082	-40060
chr1	11864535	11867082	E082	26436