Variant report

Variant	rs8025188
Chromosome Location	chr15:78912278-78912279
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:78912183-78912612	A549	lung:	n/a	n/a
2	RAD21	chr15:78912239-78912612	SK-N-SH_RA	brain:	n/a	n/a
3	SIN3A	chr15:78912061-78913606	H1-hESC	embryonic stem cell:	n/a	chr15:78913496-78913504 chr15:78913431-78913444 chr15:78912568-78912577 chr15:78912811-78912820 chr15:78913494-78913503
4	TBP	chr15:78912176-78913641	H1-hESC	embryonic stem cell:	n/a	n/a
5	ZNF263	chr15:78912234-78913094	HEK293-T-REx	kidney:	n/a	n/a
6	CTCF	chr15:78912228-78912670	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr15:78910459-78912794	SK-N-SH	brain:	n/a	chr15:78910923-78910933 chr15:78910923-78910935 chr15:78910918-78910937 chr15:78910921-78910934
8	REST	chr15:78912215-78912652	SK-N-SH	brain:	n/a	chr15:78912520-78912533
9	CTCF	chr15:78911380-78913438	SK-N-SH	brain:	n/a	n/a
10	CTBP2	chr15:78912095-78913423	H1-hESC	embryonic stem cell:	n/a	n/a
11	GABPA	chr15:78912172-78912836	H1-hESC	embryonic stem cell:	n/a	n/a
12	E2F6	chr15:78912181-78913681	H1-hESC	embryonic stem cell:	n/a	chr15:78913177-78913186 chr15:78912686-78912700
13	CTCF	chr15:78911682-78913196	A549	lung:	n/a	n/a
14	EP300	chr15:78909743-78912912	SK-N-SH	brain:	n/a	chr15:78911009-78911018 chr15:78911795-78911811
15	CTCF	chr15:78912225-78912726	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr15:78910468-78914011	SK-N-SH	brain:	n/a	n/a
17	E2F6	chr15:78912256-78912924	A549	lung:	n/a	chr15:78912686-78912700
18	RAD21	chr15:78912197-78912696	H1-hESC	embryonic stem cell:	n/a	n/a
19	GABPA	chr15:78912251-78912759	H1-hESC	embryonic stem cell:	n/a	n/a
20	CHD1	chr15:78912275-78912724	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78910619..78912332-chr15:78931297..78933969,3	MCF-7	breast:

Variant related genes	Relation type
CHRNA3	TF binding region
ENSG00000117971	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12901300	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911602	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1878399	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3743077	0.91[EUR][1000 genomes]
rs481134	0.89[EUR][1000 genomes]
rs555018	0.89[EUR][1000 genomes]
rs588765	0.87[EUR][1000 genomes]
rs601079	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs621849	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs647041	0.90[EUR][1000 genomes]
rs6495306	0.87[EUR][1000 genomes]
rs6495307	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs680244	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3395709	chr15:78911922-78914770	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs8025188	CHRNA5	cis	Nerve Tibial	GTEx
rs8025188	CHRNA5	cis	Esophagus Mucosa	GTEx
rs8025188	CHRNA5	cis	Heart Left Ventricle	GTEx
rs8025188	CHRNA5	cis	lung	GTEx
rs8025188	RP11-650L12.2	cis	Esophagus Mucosa	GTEx
rs8025188	CHRNA3	cis	Muscle Skeletal	GTEx
rs8025188	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs8025188	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs8025188	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs8025188	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs8025188	CHRNA5	cis	Muscle Skeletal	GTEx
rs8025188	RP11-650L12.2	cis	lung	GTEx
rs8025188	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78910000-78912600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr15:78911000-78912600	Bivalent Enhancer	Fetal Heart	heart
3	chr15:78911000-78912800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
4	chr15:78911000-78914200	Active TSS	Thymus	Thymus
5	chr15:78911400-78912400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
6	chr15:78911400-78914600	Bivalent Enhancer	Placenta	Placenta
7	chr15:78911600-78912600	Bivalent Enhancer	Esophagus	oesophagus
8	chr15:78911600-78913200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
9	chr15:78911600-78913600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
10	chr15:78911800-78912400	Bivalent Enhancer	A549	lung
11	chr15:78911800-78913800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:78911800-78913800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr15:78911800-78913800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
14	chr15:78912000-78912400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
15	chr15:78912000-78912400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:78912000-78912400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
17	chr15:78912000-78912400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
18	chr15:78912000-78912400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:78912000-78912400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
20	chr15:78912000-78912600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr15:78912000-78912600	Enhancers	Pancreas	Pancrea
22	chr15:78912000-78912800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
23	chr15:78912000-78913000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr15:78912000-78913000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
25	chr15:78912000-78913000	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr15:78912000-78913200	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr15:78912000-78913600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr15:78912000-78913600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:78912000-78913600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:78912000-78913600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:78912000-78913600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
32	chr15:78912000-78913800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr15:78912000-78914400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
34	chr15:78912200-78912400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:78912200-78912400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:78912200-78912400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:78912200-78912400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
38	chr15:78912200-78912400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:78912200-78912400	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
40	chr15:78912200-78912400	Bivalent Enhancer	HepG2	liver
41	chr15:78912200-78912600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr15:78912200-78912600	Bivalent Enhancer	Liver	Liver
43	chr15:78912200-78912600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
44	chr15:78912200-78912800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
45	chr15:78912200-78912800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
46	chr15:78912200-78913000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:78912200-78913000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
48	chr15:78912200-78913000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
49	chr15:78912200-78913000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
50	chr15:78912200-78913200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood

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