SNP Detail Info-rs11260542

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.1174639A>G
GRCh37.p13 chr 1	NC_000001.10:g.1110019A>G

Molecule type	Change	Amino acid[Codon]	SO Term
TTLL10 transcript variant 1	NM_001130045.1:c.	N/A	Intron Variant
TTLL10 transcript variant 2	NM_153254.2:c.	N/A	Genic Upstream Transcript Variant
TTLL10 transcript variant X7	XM_011541177.2:c.	N/A	Intron Variant
TTLL10 transcript variant X10	XM_005244738.1:c.	N/A	Genic Upstream Transcript Variant
TTLL10 transcript variant X1	XM_017000906.1:c.	N/A	Genic Upstream Transcript Variant
TTLL10 transcript variant X2	XM_017000907.1:c.	N/A	Genic Upstream Transcript Variant
TTLL10 transcript variant X3	XM_017000908.1:c.	N/A	Genic Upstream Transcript Variant
TTLL10 transcript variant X4	XM_017000909.1:c.	N/A	Genic Upstream Transcript Variant
TTLL10 transcript variant X5	XM_017000910.1:c.	N/A	Genic Upstream Transcript Variant
TTLL10 transcript variant X6	XM_017000911.1:c.	N/A	Genic Upstream Transcript Variant
TTLL10 transcript variant X8	XM_017000912.1:c.	N/A	Genic Upstream Transcript Variant
TTLL10 transcript variant X11	XR_001737089.1:n.	N/A	Intron Variant
TTLL10 transcript variant X9	XR_001737088.1:n.	N/A	Genic Upstream Transcript Variant

Molecule type	Change	Amino acid[Codon]	SO Term
TTLL10-AS1 transcript variant X2	XR_132470.6:n.204...XR_132470.6:n.2042T>C	T>C	Non Coding Transcript Variant
TTLL10-AS1 transcript variant X1	XR_946813.2:n.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.720	G=0.280
1000Genomes	American	Sub	694	A=0.940	G=0.060
1000Genomes	East Asian	Sub	1008	A=0.874	G=0.126
1000Genomes	Europe	Sub	1006	A=0.915	G=0.085
1000Genomes	Global	Study-wide	5008	A=0.855	G=0.145
1000Genomes	South Asian	Sub	978	A=0.900	G=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.910	G=0.090
The Genome Aggregation Database	African	Sub	8712	A=0.751	G=0.249
The Genome Aggregation Database	American	Sub	838	A=0.940	G=0.060
The Genome Aggregation Database	East Asian	Sub	1622	A=0.900	G=0.100
The Genome Aggregation Database	Europe	Sub	18480	A=0.895	G=0.104
The Genome Aggregation Database	Global	Study-wide	29954	A=0.854	G=0.145
The Genome Aggregation Database	Other	Sub	302	A=0.900	G=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.844	G=0.155
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.906	G=0.094

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs11260542	0.000824	alcohol dependence	20201924

eQTL of rs11260542 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:1110019	TTLL10-AS1	ENSG00000205231.1	A>G	1.6930e-8	-4916	Caudate_basal_ganglia
Chr1:1110019	TTLL10	ENSG00000162571.9	A>G	1.8731e-3	-4550	Putamen_basal_ganglia
Chr1:1110019	TTLL10-AS1	ENSG00000205231.1	A>G	2.6159e-6	-4916	Putamen_basal_ganglia
Chr1:1110019	ATAD3B	ENSG00000160072.15	A>G	9.4871e-12	-297124	Putamen_basal_ganglia
Chr1:1110019	TTLL10	ENSG00000162571.9	A>G	2.3570e-2	-4550	Nucleus_accumbens_basal_ganglia

Probe ID	Position	Gene	beta	p-value
cg10143960	chr1:1109486	TTLL10	0.158326251981881	2.5673e-32
cg01961752	chr1:1109012	TTLL10	0.048846522984577	2.7681e-10

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	1094384	1094466	E067	-15553
chr1	1118689	1118886	E067	8670
chr1	1119460	1119525	E067	9441
chr1	1120494	1120645	E067	10475
chr1	1120756	1120865	E067	10737
chr1	1094384	1094466	E068	-15553
chr1	1120494	1120645	E068	10475
chr1	1120756	1120865	E068	10737
chr1	1094384	1094466	E069	-15553
chr1	1120494	1120645	E069	10475
chr1	1120756	1120865	E069	10737
chr1	1143415	1144181	E069	33396
chr1	1144374	1144552	E069	34355
chr1	1070290	1070359	E070	-39660
chr1	1120494	1120645	E071	10475
chr1	1120756	1120865	E071	10737
chr1	1140734	1140952	E071	30715
chr1	1143415	1144181	E071	33396
chr1	1089186	1089253	E072	-20766
chr1	1089335	1089583	E072	-20436
chr1	1092283	1092675	E072	-17344
chr1	1094384	1094466	E072	-15553
chr1	1118689	1118886	E072	8670
chr1	1119460	1119525	E072	9441
chr1	1120494	1120645	E072	10475
chr1	1120756	1120865	E072	10737
chr1	1143415	1144181	E072	33396
chr1	1144374	1144552	E072	34355
chr1	1094384	1094466	E073	-15553
chr1	1092283	1092675	E074	-17344
chr1	1094384	1094466	E074	-15553
chr1	1118689	1118886	E074	8670
chr1	1120494	1120645	E074	10475
chr1	1120756	1120865	E074	10737
chr1	1070290	1070359	E081	-39660
chr1	1070674	1071648	E081	-38371
chr1	1071730	1073509	E081	-36510
chr1	1094384	1094466	E081	-15553
chr1	1143415	1144181	E081	33396
chr1	1144374	1144552	E081	34355
chr1	1143415	1144181	E082	33396

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	1092784	1094167	E067	-15852
chr1	1092784	1094167	E068	-15852
chr1	1092784	1094167	E069	-15852
chr1	1136717	1137192	E069	26698
chr1	1092784	1094167	E070	-15852
chr1	1136024	1136620	E070	26005
chr1	1136717	1137192	E070	26698
chr1	1092784	1094167	E071	-15852
chr1	1136024	1136620	E071	26005
chr1	1136717	1137192	E071	26698
chr1	1092784	1094167	E072	-15852
chr1	1092784	1094167	E073	-15852
chr1	1092784	1094167	E074	-15852
chr1	1092784	1094167	E082	-15852
chr1	1136024	1136620	E082	26005
chr1	1136717	1137192	E082	26698

rs11260542