Variant report

Variant	rs61749208
Chromosome Location	chr9:116356776-116356777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr9:116355987-116356800	A549	lung:	n/a	n/a
2	POLR2A	chr9:116355854-116363729	IMR90	lung:	n/a	n/a
3	RAD21	chr9:116356002-116356791	SK-N-SH_RA	brain:	n/a	n/a
4	CHD1	chr9:116355774-116358399	IMR90	lung:	n/a	n/a
5	RAD21	chr9:116355872-116357284	IMR90	lung:	n/a	chr9:116357082-116357095
6	POLR2A	chr9:116355972-116357585	GM12878	blood:	n/a	n/a
7	JUND	chr9:116356004-116356799	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr9:116355824-116356891	SK-N-SH	brain:	n/a	n/a
9	MXI1	chr9:116355672-116358401	IMR90	lung:	n/a	n/a
10	MXI1	chr9:116355468-116357785	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr9:116355839-116363936	U87	brain:	n/a	n/a
12	MEF2A	chr9:116355730-116356778	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr9:116355847-116358464	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr9:116356029-116357109	HUVEC	blood vessel:	n/a	n/a
15	MAX	chr9:116355930-116356850	A549	lung:	n/a	chr9:116356274-116356284
16	POLR2A	chr9:116355884-116358392	U87	brain:	n/a	n/a
17	SIN3A	chr9:116355907-116356860	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr9:116355828-116358347	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr9:116355884-116363272	U87	brain:	n/a	n/a
20	REST	chr9:116355992-116356868	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr9:116355946-116358394	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr9:116355722-116357055	GM12878	blood:	n/a	n/a
23	POLR2A	chr9:116355988-116356933	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr9:116356037-116356880	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr9:116355926-116356793	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr9:116355845-116363433	U87	brain:	n/a	n/a
27	POLR2A	chr9:116355683-116363234	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr9:116355816-116357389	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF12	chr9:116356024-116357103	A549	lung:	n/a	chr9:116356984-116356994
30	EBF1	chr9:116356730-116356989	GM12878	blood:	n/a	chr9:116356858-116356867 chr9:116356856-116356869
31	EP300	chr9:116355851-116357074	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr9:116355897-116365640	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr9:116356094-116356776	Gliobla	brain:	n/a	n/a
34	EP300	chr9:116355873-116356802	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr9:116356099-116356826	ProgFib	skin:	n/a	n/a
36	MAZ	chr9:116355779-116358015	IMR90	lung:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf43-6	chr9:116356424-116356811	NONHSAT134355

No data

Variant related genes	Relation type
ENSG00000237073	TF binding region
RGS3	TF binding region

Extended variants
information (count: 180 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:171)

rs_ID	r²[population]
rs10116799	0.89[EUR][1000 genomes]
rs10125960	0.91[EUR][1000 genomes]
rs10217341	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10481676	0.91[EUR][1000 genomes]
rs10481677	0.91[EUR][1000 genomes]
rs10981789	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10981803	0.91[EUR][1000 genomes]
rs10981807	0.91[EUR][1000 genomes]
rs10981808	0.91[EUR][1000 genomes]
rs10981814	0.91[EUR][1000 genomes]
rs10981816	0.91[EUR][1000 genomes]
rs10981817	0.91[EUR][1000 genomes]
rs10981819	0.91[EUR][1000 genomes]
rs10981820	0.91[EUR][1000 genomes]
rs10981821	0.91[EUR][1000 genomes]
rs10981825	0.94[EUR][1000 genomes]
rs10981826	0.94[EUR][1000 genomes]
rs10981827	0.94[EUR][1000 genomes]
rs10981828	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10981829	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10981831	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10981832	0.93[EUR][1000 genomes]
rs10981839	0.82[EUR][1000 genomes]
rs12335716	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12336719	0.91[EUR][1000 genomes]
rs12337340	0.96[EUR][1000 genomes]
rs12338588	0.91[EUR][1000 genomes]
rs12338697	0.96[EUR][1000 genomes]
rs12338701	0.96[EUR][1000 genomes]
rs12339493	0.96[EUR][1000 genomes]
rs12339501	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12339617	0.91[EUR][1000 genomes]
rs12340996	0.91[EUR][1000 genomes]
rs12341332	0.96[EUR][1000 genomes]
rs12341490	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12342508	0.91[EUR][1000 genomes]
rs12342699	0.91[EUR][1000 genomes]
rs12343129	0.96[EUR][1000 genomes]
rs12343141	0.91[EUR][1000 genomes]
rs12343940	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12344334	0.94[EUR][1000 genomes]
rs12344578	0.91[EUR][1000 genomes]
rs12345524	0.91[EUR][1000 genomes]
rs12345968	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12346076	0.91[EUR][1000 genomes]
rs12346087	0.96[EUR][1000 genomes]
rs12346939	0.91[EUR][1000 genomes]
rs12347895	0.96[EUR][1000 genomes]
rs12348214	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12348239	0.96[EUR][1000 genomes]
rs12349661	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12353541	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1890992	0.94[EUR][1000 genomes]
rs2050865	0.91[EUR][1000 genomes]
rs2050866	0.90[EUR][1000 genomes]
rs28594159	0.93[EUR][1000 genomes]
rs28694002	0.91[EUR][1000 genomes]
rs28714985	0.91[EUR][1000 genomes]
rs35270441	0.91[EUR][1000 genomes]
rs35358414	0.81[EUR][1000 genomes]
rs35533905	0.81[EUR][1000 genomes]
rs3983381	0.94[EUR][1000 genomes]
rs41301525	0.96[EUR][1000 genomes]
rs41305473	0.92[EUR][1000 genomes]
rs41313331	0.89[EUR][1000 genomes]
rs4596719	0.91[EUR][1000 genomes]
rs55676913	0.91[EUR][1000 genomes]
rs55696921	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55777057	0.94[EUR][1000 genomes]
rs55805468	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55931715	0.94[EUR][1000 genomes]
rs55977108	0.91[EUR][1000 genomes]
rs56155263	0.94[EUR][1000 genomes]
rs56276438	0.94[EUR][1000 genomes]
rs56390346	0.94[EUR][1000 genomes]
rs6478011	0.89[EUR][1000 genomes]
rs6478016	0.91[EUR][1000 genomes]
rs6478022	0.94[EUR][1000 genomes]
rs6478023	0.94[EUR][1000 genomes]
rs7018783	0.91[EUR][1000 genomes]
rs7020623	0.91[EUR][1000 genomes]
rs7021688	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7023661	0.91[EUR][1000 genomes]
rs7024445	0.94[EUR][1000 genomes]
rs7024612	0.94[EUR][1000 genomes]
rs7024996	0.94[EUR][1000 genomes]
rs7025170	0.94[EUR][1000 genomes]
rs7025745	0.91[EUR][1000 genomes]
rs7026568	0.91[EUR][1000 genomes]
rs7026656	0.91[EUR][1000 genomes]
rs7027024	0.91[EUR][1000 genomes]
rs7027340	0.91[EUR][1000 genomes]
rs7028327	0.91[EUR][1000 genomes]
rs7029685	0.91[EUR][1000 genomes]
rs7032311	0.93[EUR][1000 genomes]
rs7037441	0.91[EUR][1000 genomes]
rs7040031	0.91[EUR][1000 genomes]
rs7041833	0.91[EUR][1000 genomes]
rs7042290	0.91[EUR][1000 genomes]
rs7042695	0.91[EUR][1000 genomes]
rs7043140	0.91[EUR][1000 genomes]
rs7043571	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7045347	0.91[EUR][1000 genomes]
rs7046202	0.89[EUR][1000 genomes]
rs7046427	0.91[EUR][1000 genomes]
rs7047062	0.96[EUR][1000 genomes]
rs7048208	0.96[EUR][1000 genomes]
rs7048305	0.89[EUR][1000 genomes]
rs72760092	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72760093	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72760097	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72761903	0.90[EUR][1000 genomes]
rs72761904	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72761966	0.91[EUR][1000 genomes]
rs72761968	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761972	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761982	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761985	0.93[EUR][1000 genomes]
rs72761987	0.91[EUR][1000 genomes]
rs72761988	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72761992	0.91[EUR][1000 genomes]
rs72761994	0.91[EUR][1000 genomes]
rs72761997	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72762002	0.90[EUR][1000 genomes]
rs72763803	0.91[EUR][1000 genomes]
rs72763804	0.91[EUR][1000 genomes]
rs72763806	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72763816	0.94[EUR][1000 genomes]
rs72763826	0.96[EUR][1000 genomes]
rs72763827	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72763828	0.96[EUR][1000 genomes]
rs72763831	0.96[EUR][1000 genomes]
rs72763832	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72763842	0.96[EUR][1000 genomes]
rs72763843	0.96[EUR][1000 genomes]
rs72763846	0.96[EUR][1000 genomes]
rs72763848	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72763849	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72763851	0.84[EUR][1000 genomes]
rs72763859	0.82[EUR][1000 genomes]
rs72763861	0.82[EUR][1000 genomes]
rs7848203	0.89[EUR][1000 genomes]
rs7849841	0.89[EUR][1000 genomes]
rs7851718	0.91[EUR][1000 genomes]
rs7853373	0.91[EUR][1000 genomes]
rs7853792	0.91[EUR][1000 genomes]
rs7854197	0.91[EUR][1000 genomes]
rs7855325	0.91[EUR][1000 genomes]
rs7856515	0.93[EUR][1000 genomes]
rs7857943	0.96[EUR][1000 genomes]
rs7859047	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7860673	0.91[EUR][1000 genomes]
rs7861248	0.89[EUR][1000 genomes]
rs7863159	0.96[EUR][1000 genomes]
rs7864645	0.89[EUR][1000 genomes]
rs7865364	0.96[EUR][1000 genomes]
rs7867353	0.91[EUR][1000 genomes]
rs7870227	0.91[EUR][1000 genomes]
rs7870451	0.87[EUR][1000 genomes]
rs7871186	0.96[EUR][1000 genomes]
rs7872084	0.90[EUR][1000 genomes]
rs7872192	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7872283	0.91[EUR][1000 genomes]
rs867375	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs884899	0.96[EUR][1000 genomes]
rs9299215	0.91[EUR][1000 genomes]
rs944345	0.96[EUR][1000 genomes]
rs944346	0.96[EUR][1000 genomes]
rs9657641	0.96[EUR][1000 genomes]
rs9657658	0.96[EUR][1000 genomes]
rs9657659	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription 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	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	nsv466509	chr9:116356516-116396098	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv615216	chr9:116356516-116396098	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116343200-116358800	Weak transcription	Hela-S3	cervix
2	chr9:116346600-116356800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr9:116348000-116361600	Weak transcription	Dnd41	blood
4	chr9:116352200-116357400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:116352400-116357000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:116352400-116357600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr9:116352400-116358000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:116352400-116363200	Weak transcription	Thymus	Thymus
9	chr9:116352600-116357000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr9:116353200-116361000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr9:116353200-116361400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr9:116353400-116361400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:116353800-116360400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:116354200-116356800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr9:116354800-116357000	Weak transcription	Primary T cells from cord blood	blood
16	chr9:116355200-116357200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:116355600-116357000	Enhancers	Primary B cells from cord blood	blood
18	chr9:116355800-116357000	Flanking Active TSS	Fetal Muscle Leg	muscle
19	chr9:116355800-116357000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr9:116355800-116357200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:116355800-116357200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:116355800-116357400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr9:116355800-116357400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr9:116355800-116357400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:116355800-116357400	Flanking Active TSS	Brain Cingulate Gyrus	brain
26	chr9:116355800-116357400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr9:116355800-116357400	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr9:116355800-116357600	Enhancers	Fetal Brain Male	brain
29	chr9:116355800-116357600	Active TSS	Right Ventricle	heart
30	chr9:116355800-116357600	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr9:116355800-116357800	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr9:116355800-116357800	Enhancers	Stomach Mucosa	stomach
33	chr9:116355800-116360800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr9:116355800-116360800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr9:116356000-116356800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:116356000-116357000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr9:116356000-116357000	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr9:116356000-116357000	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr9:116356000-116357200	Active TSS	H9 Cell Line	embryonic stem cell
40	chr9:116356000-116357200	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr9:116356000-116357200	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr9:116356000-116357400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr9:116356000-116357400	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr9:116356000-116357400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr9:116356000-116357400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr9:116356000-116357400	Flanking Active TSS	HepG2	liver
47	chr9:116356000-116357600	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr9:116356000-116357600	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr9:116356000-116357600	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr9:116356000-116358000	Active TSS	Colon Smooth Muscle	Colon

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