SNP Detail Info-rs6672508

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.41200899C>G
GRCh38.p7 chr 1	NC_000001.11:g.41200899C>T
GRCh37.p13 chr 1	NC_000001.10:g.41666571C>G
GRCh37.p13 chr 1	NC_000001.10:g.41666571C>T

Gene: SCMH1, sex comb on midleg homolog 1 (Drosophila)(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCMH1 transcript variant 3	NM_001172218.1:c.	N/A	Intron Variant
SCMH1 transcript variant 4	NM_001172219.1:c.	N/A	Intron Variant
SCMH1 transcript variant 5	NM_001172220.1:c.	N/A	Intron Variant
SCMH1 transcript variant 2	NM_012236.3:c.	N/A	Intron Variant
SCMH1 transcript variant 1	NM_001031694.2:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant 6	NM_001172221.1:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant 7	NM_001172222.2:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant 8	NR_135092.1:n.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X1	XM_006710462.2:c.	N/A	Intron Variant
SCMH1 transcript variant X3	XM_011541033.2:c.	N/A	Intron Variant
SCMH1 transcript variant X4	XM_011541034.1:c.	N/A	Intron Variant
SCMH1 transcript variant X6	XM_011541035.2:c.	N/A	Intron Variant
SCMH1 transcript variant X8	XM_011541036.2:c.	N/A	Intron Variant
SCMH1 transcript variant X18	XM_011541039.1:c.	N/A	Intron Variant
SCMH1 transcript variant X21	XM_011541040.2:c.	N/A	Intron Variant
SCMH1 transcript variant X28	XM_011541043.2:c.	N/A	Intron Variant
SCMH1 transcript variant X14	XM_011541045.2:c.	N/A	Intron Variant
SCMH1 transcript variant X9	XM_017000699.1:c.	N/A	Intron Variant
SCMH1 transcript variant X15	XM_017000700.1:c.	N/A	Intron Variant
SCMH1 transcript variant X15	XM_017000701.1:c.	N/A	Intron Variant
SCMH1 transcript variant X19	XM_017000702.1:c.	N/A	Intron Variant
SCMH1 transcript variant X20	XM_017000703.1:c.	N/A	Intron Variant
SCMH1 transcript variant X19	XM_017000704.1:c.	N/A	Intron Variant
SCMH1 transcript variant X25	XM_017000705.1:c.	N/A	Intron Variant
SCMH1 transcript variant X30	XM_017000706.1:c.	N/A	Intron Variant
SCMH1 transcript variant X31	XM_017000707.1:c.	N/A	Intron Variant
SCMH1 transcript variant X32	XM_017000712.1:c.	N/A	Intron Variant
SCMH1 transcript variant X37	XM_017000713.1:c.	N/A	Intron Variant
SCMH1 transcript variant X7	XM_006710464.1:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X2	XM_011541032.2:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X29	XM_011541044.1:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X5	XM_017000698.1:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X30	XM_017000708.1:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X33	XM_017000709.1:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X34	XM_017000710.1:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X31	XM_017000711.1:c.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X13	XR_001737045.1:n.	N/A	Intron Variant
SCMH1 transcript variant X17	XR_001737046.1:n.	N/A	Intron Variant
SCMH1 transcript variant X21	XR_001737047.1:n.	N/A	Intron Variant
SCMH1 transcript variant X22	XR_001737048.1:n.	N/A	Intron Variant
SCMH1 transcript variant X23	XR_001737049.1:n.	N/A	Intron Variant
SCMH1 transcript variant X24	XR_001737050.1:n.	N/A	Intron Variant
SCMH1 transcript variant X26	XR_001737051.1:n.	N/A	Intron Variant
SCMH1 transcript variant X34	XR_001737053.1:n.	N/A	Intron Variant
SCMH1 transcript variant X10	XR_946584.2:n.	N/A	Intron Variant
SCMH1 transcript variant X27	XR_001737052.1:n.	N/A	Genic Upstream Transcript Variant
SCMH1 transcript variant X35	XR_001737054.1:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.912	G=0.088
1000Genomes	American	Sub	694	C=0.700	G=0.300
1000Genomes	East Asian	Sub	1008	C=0.832	G=0.168
1000Genomes	Europe	Sub	1006	C=0.696	G=0.304
1000Genomes	Global	Study-wide	5008	C=0.797	G=0.203
1000Genomes	South Asian	Sub	978	C=0.770	G=0.230
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.678	G=0.322
The Genome Aggregation Database	African	Sub	8710	C=0.877	G=0.123
The Genome Aggregation Database	American	Sub	832	C=0.710	G=0.29,
The Genome Aggregation Database	East Asian	Sub	1610	C=0.886	G=0.114
The Genome Aggregation Database	Europe	Sub	18344	C=0.688	G=0.311
The Genome Aggregation Database	Global	Study-wide	29796	C=0.754	G=0.245
The Genome Aggregation Database	Other	Sub	300	C=0.700	G=0.30,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.774	G=0.225
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.675	G=0.325

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs6672508	0.000953	alcohol dependence	21314694

eQTL of rs6672508 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:41666571	RP11-399E6.1	ENSG00000235358.1	C>G	6.4919e-3	-41474	Putamen_basal_ganglia

meQTL of rs6672508 in Fetal Brain

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

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	185123993	185124068	E067	13999
chr1	185124318	185124510	E067	14324
chr1	185127709	185127893	E067	17715
chr1	185127968	185128414	E067	17974
chr1	185123993	185124068	E068	13999
chr1	185124165	185124229	E068	14171
chr1	185124318	185124510	E068	14324
chr1	185127709	185127893	E068	17715
chr1	185127968	185128414	E068	17974
chr1	185123134	185123224	E069	13140
chr1	185123605	185123749	E069	13611
chr1	185123993	185124068	E069	13999
chr1	185124165	185124229	E069	14171
chr1	185124318	185124510	E069	14324
chr1	185127709	185127893	E069	17715
chr1	185123993	185124068	E071	13999
chr1	185124165	185124229	E071	14171
chr1	185124318	185124510	E071	14324
chr1	185127968	185128414	E071	17974
chr1	185127709	185127893	E072	17715
chr1	185127968	185128414	E072	17974
chr1	185124165	185124229	E073	14171
chr1	185127709	185127893	E073	17715
chr1	185127968	185128414	E073	17974
chr1	185124318	185124510	E074	14324
chr1	185127709	185127893	E074	17715
chr1	185127968	185128414	E074	17974
chr1	185128524	185128574	E081	18530
chr1	185124318	185124510	E082	14324

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	185124867	185127572	E067	14873
chr1	185124867	185127572	E068	14873
chr1	185124867	185127572	E069	14873
chr1	185124867	185127572	E070	14873
chr1	185124867	185127572	E071	14873
chr1	185124867	185127572	E072	14873
chr1	185124867	185127572	E073	14873
chr1	185124867	185127572	E074	14873
chr1	185124867	185127572	E081	14873
chr1	185124867	185127572	E082	14873

rs6672508

Genomic Coordinates

Gene: SCMH1, sex comb on midleg homolog 1 (Drosophila)(minus strand)

Population Frequency

P-Value

eQTL of rs6672508 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs6672508 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)