Variant report

Variant	rs884992
Chromosome Location	chr9:116357408-116357409
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	POLR2A	chr9:116355854-116363729	IMR90	lung:	n/a	n/a
2	CHD1	chr9:116355774-116358399	IMR90	lung:	n/a	n/a
3	POLR2A	chr9:116355972-116357585	GM12878	blood:	n/a	n/a
4	MXI1	chr9:116355672-116358401	IMR90	lung:	n/a	n/a
5	MXI1	chr9:116355468-116357785	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr9:116355839-116363936	U87	brain:	n/a	n/a
7	POLR2A	chr9:116357120-116358308	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:116355847-116358464	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr9:116355884-116358392	U87	brain:	n/a	n/a
10	POLR2A	chr9:116357204-116358247	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr9:116355828-116358347	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr9:116355884-116363272	U87	brain:	n/a	n/a
13	POLR2A	chr9:116355946-116358394	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr9:116357340-116357490	HBMEC	blood vessel:	n/a	n/a
15	POLR2A	chr9:116355845-116363433	U87	brain:	n/a	n/a
16	POLR2A	chr9:116355683-116363234	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr9:116355897-116365640	HUVEC	blood vessel:	n/a	n/a
18	MAZ	chr9:116355779-116358015	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
RGS3	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1051013	0.88[AFR][1000 genomes]
rs10817493	0.82[AFR][1000 genomes]
rs10981818	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs10981833	0.84[ASN][1000 genomes]
rs16934489	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs6478023	0.80[YRI][hapmap]
rs7024445	0.81[YRI][hapmap]

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	chr9:116348000-116361600	Weak transcription	Dnd41	blood
3	chr9:116352400-116357600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr9:116352400-116358000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:116352400-116363200	Weak transcription	Thymus	Thymus
6	chr9:116353200-116361000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:116353200-116361400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:116353400-116361400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr9:116353800-116360400	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:116355800-116357600	Enhancers	Fetal Brain Male	brain
11	chr9:116355800-116357600	Active TSS	Right Ventricle	heart
12	chr9:116355800-116357600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr9:116355800-116357800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr9:116355800-116357800	Enhancers	Stomach Mucosa	stomach
15	chr9:116355800-116360800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:116355800-116360800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:116356000-116357600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr9:116356000-116357600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr9:116356000-116357600	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr9:116356000-116358000	Active TSS	Colon Smooth Muscle	Colon
21	chr9:116356200-116357600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:116356200-116357600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:116356200-116357600	Active TSS	Muscle Satellite Cultured Cells	--
24	chr9:116356200-116357600	Active TSS	Psoas Muscle	Psoas
25	chr9:116356200-116357600	Active TSS	Rectal Smooth Muscle	rectum
26	chr9:116356200-116357600	Active TSS	A549	lung
27	chr9:116356200-116357600	Active TSS	HSMM	muscle
28	chr9:116356200-116357600	Active TSS	NH-A	brain
29	chr9:116356200-116357600	Active TSS	NHDF-Ad	bronchial
30	chr9:116356200-116357600	Active TSS	Osteobl	bone
31	chr9:116356200-116357800	Active TSS	Fetal Kidney	kidney
32	chr9:116356200-116358000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:116356200-116358000	Active TSS	HSMMtube	muscle
34	chr9:116356200-116358200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
35	chr9:116356200-116359000	Weak transcription	Small Intestine	intestine
36	chr9:116356400-116357600	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr9:116356400-116357600	Active TSS	Liver	Liver
38	chr9:116356400-116357600	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr9:116356400-116357800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:116356400-116357800	Active TSS	Aorta	Aorta
41	chr9:116356400-116357800	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
42	chr9:116356400-116357800	Active TSS	Left Ventricle	heart
43	chr9:116356400-116360400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:116356400-116360600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
45	chr9:116356400-116361200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr9:116356600-116357600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:116356600-116357600	Active TSS	Right Atrium	heart
48	chr9:116356600-116357800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:116356600-116360800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr9:116356600-116361000	Strong transcription	Primary monocytes fromperipheralblood	blood

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