Variant report

Variant	rs2067808
Chromosome Location	chr15:78911780-78911781
allele	C/T
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	RAD21	chr15:78910459-78912794	SK-N-SH	brain:	n/a	chr15:78910923-78910933 chr15:78910923-78910935 chr15:78910918-78910937 chr15:78910921-78910934
2	CTCF	chr15:78911660-78911810	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr15:78911380-78913438	SK-N-SH	brain:	n/a	n/a
4	TEAD4	chr15:78911710-78912086	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr15:78911760-78911910	WERI-Rb-1	eye:	n/a	n/a
6	CTCF	chr15:78911682-78913196	A549	lung:	n/a	n/a
7	EP300	chr15:78909743-78912912	SK-N-SH	brain:	n/a	chr15:78911009-78911018 chr15:78911795-78911811
8	TEAD4	chr15:78911694-78912093	H1-hESC	embryonic stem cell:	n/a	n/a
9	MXI1	chr15:78910468-78914011	SK-N-SH	brain:	n/a	n/a
10	SMC3	chr15:78910312-78912084	SK-N-SH	brain:	n/a	chr15:78910919-78910927 chr15:78910919-78910933 chr15:78910923-78910933 chr15:78911911-78911918

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: 36 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11637635	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12901300	0.84[ASN][1000 genomes]
rs12911602	0.88[ASN][1000 genomes]
rs17408276	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1878399	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456019	0.84[AMR][1000 genomes]
rs2869546	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2904130	0.84[EUR][1000 genomes]
rs3743073	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3743074	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3743075	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3743077	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs471889	0.88[EUR][1000 genomes]
rs472054	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4887070	0.84[EUR][1000 genomes]
rs495090	0.88[EUR][1000 genomes]
rs495956	0.88[EUR][1000 genomes]
rs514743	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57945453	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs584135	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61012457	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs615470	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62010327	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62010328	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62010332	0.86[EUR][1000 genomes]
rs647041	0.87[ASN][1000 genomes]
rs6495307	0.87[ASN][1000 genomes]
rs660652	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs692780	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7182583	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7495518	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8023462	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2067808	CHRNA5	cis	Esophagus Mucosa	GTEx
rs2067808	CHRNA5	cis	Nerve Tibial	GTEx
rs2067808	CHRNA3	cis	Muscle Skeletal	GTEx
rs2067808	RP11-650L12.2	cis	lung	GTEx
rs2067808	CHRNA5	cis	Muscle Skeletal	GTEx
rs2067808	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs2067808	CHRNA5	cis	lung	GTEx
rs2067808	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs2067808	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs2067808	CHRNA5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78910000-78912600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr15:78910200-78912200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:78911000-78911800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
4	chr15:78911000-78911800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
5	chr15:78911000-78911800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
6	chr15:78911000-78911800	Enhancers	A549	lung
7	chr15:78911000-78912000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr15:78911000-78912000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr15:78911000-78912000	Bivalent Enhancer	Fetal Stomach	stomach
10	chr15:78911000-78912200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:78911000-78912200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:78911000-78912600	Bivalent Enhancer	Fetal Heart	heart
13	chr15:78911000-78912800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
14	chr15:78911000-78914200	Active TSS	Thymus	Thymus
15	chr15:78911200-78912000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
16	chr15:78911400-78911800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
17	chr15:78911400-78912200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
18	chr15:78911400-78912400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
19	chr15:78911400-78914600	Bivalent Enhancer	Placenta	Placenta
20	chr15:78911600-78911800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:78911600-78911800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr15:78911600-78911800	Enhancers	Rectal Smooth Muscle	rectum
23	chr15:78911600-78912000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
24	chr15:78911600-78912200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:78911600-78912200	Bivalent Enhancer	Colon Smooth Muscle	Colon
26	chr15:78911600-78912600	Bivalent Enhancer	Esophagus	oesophagus
27	chr15:78911600-78913200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
28	chr15:78911600-78913600	Bivalent/Poised TSS	Fetal Intestine Small	intestine

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