Variant report

Variant	rs55720568
Chromosome Location	chr9:117376461-117376462
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr9:117376344-117376988	GM12878	blood:	n/a	n/a
2	WRNIP1	chr9:117374148-117377038	GM12878	blood:	n/a	n/a
3	POLR2A	chr9:117372060-117376570	GM12878	blood:	n/a	n/a
4	POLR2A	chr9:117373828-117376507	GM12878	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:117374384..117377233-chr9:117400977..117403274,2	K562	blood:
2	chr9:117349294..117352043-chr9:117375229..117380114,4	MCF-7	breast:
3	chr9:117348104..117352194-chr9:117371141..117379325,14	K562	blood:
4	chr9:117346757..117362857-chr9:117372020..117377914,21	MCF-7	breast:
5	chr9:117262731..117268447-chr9:117369704..117378306,14	K562	blood:
6	chr9:117266234..117268906-chr9:117372659..117377270,6	K562	blood:
7	chr9:117301959..117303545-chr9:117375054..117376572,2	MCF-7	breast:
8	chr9:117248554..117250072-chr9:117374914..117376570,2	MCF-7	breast:
9	chr9:117263907..117271703-chr9:117371218..117376768,10	MCF-7	breast:
10	chr9:117372326..117374917-chr9:117375396..117377851,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP6V1G1-2	chr9:117374792-117377101	NONHSAT134388

No data

Variant related genes	Relation type
ENSG00000272241	TF binding region
ENSG00000136888	Chromatin interaction
ENSG00000157693	Chromatin interaction
ENSG00000095397	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs41278667	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73656157	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051544	chr9:116944940-117443031	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
2	nsv540203	chr9:116944940-117443031	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv1050991	chr9:116953739-117442999	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1046311	chr9:116953739-117447142	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
6	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv1051987	chr9:116955841-117453668	Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv466534	chr9:116956268-117455810	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
11	nsv615234	chr9:116956268-117455810	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
12	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
13	nsv615236	chr9:116958144-117455810	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
14	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
15	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
16	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
17	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
18	nsv1053756	chr9:116975934-117443031	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
19	nsv540204	chr9:116975934-117443031	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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	43 gene(s)	inside rSNPs	diseases
20	nsv1047704	chr9:116978041-117399362	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
21	nsv540205	chr9:116978041-117399362	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
22	nsv530950	chr9:117009156-117399361	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
23	nsv916139	chr9:117009169-117399454	Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
24	nsv530951	chr9:117032675-117439804	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
25	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	30 gene(s)	inside rSNPs	diseases
26	esv1008480	chr9:117373830-117388680	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117374400-117377000	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr9:117374600-117381200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:117374600-117387800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117374800-117376600	Enhancers	H9 Cell Line	embryonic stem cell
5	chr9:117374800-117377000	Enhancers	Placenta	Placenta
6	chr9:117374800-117377000	Enhancers	Ovary	ovary
7	chr9:117374800-117384000	Weak transcription	NH-A	brain
8	chr9:117374800-117384200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:117374800-117384200	Weak transcription	NHLF	lung
10	chr9:117375000-117376600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:117375000-117376800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:117375000-117377000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr9:117375000-117377000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr9:117375000-117377600	Enhancers	Primary B cells from peripheral blood	blood
15	chr9:117375000-117377600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr9:117375000-117379000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:117375000-117379000	Weak transcription	Esophagus	oesophagus
18	chr9:117375000-117379000	Weak transcription	HMEC	breast
19	chr9:117375000-117379400	Weak transcription	Gastric	stomach
20	chr9:117375000-117384200	Weak transcription	Left Ventricle	heart
21	chr9:117375000-117384200	Weak transcription	Right Atrium	heart
22	chr9:117375000-117384200	Weak transcription	A549	lung
23	chr9:117375000-117384200	Weak transcription	HSMMtube	muscle
24	chr9:117375000-117388800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:117375000-117388800	Weak transcription	Liver	Liver
26	chr9:117375000-117391200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:117375000-117405200	Weak transcription	Psoas Muscle	Psoas
28	chr9:117375000-117410400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr9:117375200-117376800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:117375200-117376800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr9:117375200-117377000	Enhancers	Colon Smooth Muscle	Colon
32	chr9:117375200-117377000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr9:117375200-117377200	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr9:117375200-117377200	Enhancers	Brain Cingulate Gyrus	brain
35	chr9:117375200-117377800	Genic enhancers	Primary monocytes fromperipheralblood	blood
36	chr9:117375200-117379000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:117375200-117380200	Weak transcription	Fetal Lung	lung
38	chr9:117375200-117381400	Weak transcription	Osteobl	bone
39	chr9:117375200-117385600	Weak transcription	Fetal Intestine Small	intestine
40	chr9:117375200-117388800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr9:117375200-117388800	Weak transcription	Aorta	Aorta
42	chr9:117375200-117388800	Weak transcription	Pancreas	Pancrea
43	chr9:117375200-117389800	Weak transcription	Fetal Brain Male	brain
44	chr9:117375200-117405400	Weak transcription	Small Intestine	intestine
45	chr9:117375400-117377000	Enhancers	Adipose Nuclei	Adipose
46	chr9:117375400-117377800	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr9:117375400-117379000	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:117375400-117379200	Weak transcription	Thymus	Thymus
49	chr9:117375400-117389800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr9:117375600-117378800	Weak transcription	Duodenum Mucosa	Duodenum

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