SNP Detail Info-rs11870068

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 17	NC_000017.11:g.67948399A>C
GRCh37.p13 chr 17 fix patch HG747_PATCH	NW_003871088.1:g.8410A>C
GRCh37.p13 chr 17	NC_000017.10:g.65944515A>C

Gene: BPTF, bromodomain PHD finger transcription factor(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BPTF transcript variant 2	NM_004459.6:c.	N/A	Intron Variant
BPTF transcript variant 1	NM_182641.3:c.	N/A	Intron Variant
BPTF transcript variant X1	XM_005257150.3:c.	N/A	Intron Variant
BPTF transcript variant X3	XM_005257151.3:c.	N/A	Intron Variant
BPTF transcript variant X4	XM_005257152.2:c.	N/A	Intron Variant
BPTF transcript variant X5	XM_005257153.3:c.	N/A	Intron Variant
BPTF transcript variant X6	XM_005257154.3:c.	N/A	Intron Variant
BPTF transcript variant X7	XM_005257155.3:c.	N/A	Intron Variant
BPTF transcript variant X8	XM_005257156.3:c.	N/A	Intron Variant
BPTF transcript variant X9	XM_005257157.3:c.	N/A	Intron Variant
BPTF transcript variant X13	XM_005257158.3:c.	N/A	Intron Variant
BPTF transcript variant X15	XM_005257159.2:c.	N/A	Intron Variant
BPTF transcript variant X18	XM_005257160.2:c.	N/A	Intron Variant
BPTF transcript variant X19	XM_005257161.3:c.	N/A	Intron Variant
BPTF transcript variant X2	XM_011524520.2:c.	N/A	Intron Variant
BPTF transcript variant X10	XM_011524521.2:c.	N/A	Intron Variant
BPTF transcript variant X14	XM_011524522.2:c.	N/A	Intron Variant
BPTF transcript variant X17	XM_011524523.2:c.	N/A	Intron Variant
BPTF transcript variant X19	XM_011524524.2:c.	N/A	Intron Variant
BPTF transcript variant X23	XM_011524525.2:c.	N/A	Intron Variant
BPTF transcript variant X24	XM_011524526.2:c.	N/A	Intron Variant
BPTF transcript variant X11	XM_017024353.1:c.	N/A	Intron Variant
BPTF transcript variant X18	XM_017024354.1:c.	N/A	Intron Variant
BPTF transcript variant X22	XR_001752449.1:n.	N/A	Genic Downstream Transcript Variant
BPTF transcript variant X21	XR_001752450.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.837	C=0.163
1000Genomes	American	Sub	694	A=0.730	C=0.270
1000Genomes	East Asian	Sub	1008	A=0.307	C=0.693
1000Genomes	Europe	Sub	1006	A=0.784	C=0.216
1000Genomes	Global	Study-wide	5008	A=0.684	C=0.316
1000Genomes	South Asian	Sub	978	A=0.730	C=0.270
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.806	C=0.194
The Genome Aggregation Database	African	Sub	8716	A=0.832	C=0.168
The Genome Aggregation Database	American	Sub	838	A=0.690	C=0.310
The Genome Aggregation Database	East Asian	Sub	1618	A=0.340	C=0.660
The Genome Aggregation Database	Europe	Sub	18488	A=0.788	C=0.212
The Genome Aggregation Database	Global	Study-wide	29962	A=0.774	C=0.225
The Genome Aggregation Database	Other	Sub	302	A=0.820	C=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.815	C=0.184
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.797	C=0.203

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res
27151647	An association study revealed substantial effects of dominance, epistasis and substance dependence co-morbidity on alcohol dependence symptom count.	Chen G	Addict Biol
20202923	A genome-wide association study of alcohol dependence.	Bierut LJ	Proc Natl Acad Sci U S A
21956439	Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.	Zuo L	Neuropsychopharmacology

P-Value

SNP ID	p-value	Traits	Study
rs11870068	5.00E-07	alcohol dependence	27151647
rs11870068	0.00000767	alcohol dependence	20202923
rs11870068	0.0000809	alcohol dependence	21703634
rs11870068	0.00036	alcohol dependence	21956439

eQTL of rs11870068 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr17:65944515	BPTF	ENSG00000171634.12	A>C	1.8755e-7	122875	Cerebellum

meQTL of rs11870068 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 )
chr17	49643	49733	E067	41233
chr17	14162	14761	E068	5752
chr17	28404	28803	E068	19994
chr17	28864	29097	E068	20454
chr17	49451	49534	E069	41041
chr17	49562	49631	E069	41152
chr17	49643	49733	E069	41233
chr17	23032	23149	E070	14622
chr17	23245	23554	E070	14835
chr17	28404	28803	E070	19994
chr17	28864	29097	E070	20454
chr17	54647	54704	E070	46237
chr17	54763	54935	E070	46353
chr17	55020	55111	E070	46610
chr17	55190	55325	E070	46780
chr17	57476	57526	E070	49066
chr17	57545	57621	E070	49135
chr17	57659	57703	E070	49249
chr17	33241	33327	E073	24831
chr17	49451	49534	E073	41041
chr17	49562	49631	E073	41152
chr17	49643	49733	E073	41233
chr17	49762	50714	E073	41352
chr17	28404	28803	E081	19994
chr17	28864	29097	E081	20454
chr17	43936	44261	E081	35526
chr17	44316	44501	E081	35906
chr17	37133	37193	E082	28723

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr17	29545	29660	E068	21135
chr17	29710	30997	E068	21300
chr17	31150	31229	E068	22740
chr17	29710	30997	E069	21300
chr17	31150	31229	E069	22740
chr17	29545	29660	E070	21135
chr17	29710	30997	E070	21300
chr17	31150	31229	E070	22740
chr17	29710	30997	E071	21300
chr17	29545	29660	E072	21135
chr17	29710	30997	E072	21300
chr17	29545	29660	E073	21135
chr17	29710	30997	E073	21300
chr17	31150	31229	E073	22740
chr17	29545	29660	E074	21135
chr17	29710	30997	E082	21300
chr17	31150	31229	E082	22740

rs11870068

Genomic Coordinates

Gene: BPTF, bromodomain PHD finger transcription factor(plus strand)

Population Frequency

P-Value

eQTL of rs11870068 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs11870068 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)