Variant report

Variant	rs558654590
Chromosome Location	chr9:140498756-140498757
allele	A/G
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:13)
LncRNA
region (count:0)
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	HCFC1	chr9:140498594-140502431	Hela-S3	cervix:	n/a	n/a
2	ZNF263	chr9:140498663-140498975	HEK293-T-REx	kidney:	n/a	chr9:140498677-140498686
3	POLR2A	chr9:140498752-140498776	MCF-7	breast:	n/a	n/a
4	POLR2A	chr9:140498743-140499028	MCF-7	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:140470445..140476327-chr9:140498022..140503450,9	K562	blood:
2	chr9:140498043..140499599-chr9:140558636..140561270,2	MCF-7	breast:
3	chr9:140444055..140447780-chr9:140498087..140502451,7	MCF-7	breast:
4	chr9:140491452..140494377-chr9:140498511..140500095,2	K562	blood:
5	chr9:140443433..140448155-chr9:140497818..140502870,8	MCF-7	breast:
6	chr9:140477211..140479524-chr9:140496943..140498868,3	K562	blood:
7	chr9:140482616..140489091-chr9:140495925..140503345,17	MCF-7	breast:
8	chr9:140482416..140489757-chr9:140495738..140502746,21	K562	blood:
9	chr9:140447049..140448753-chr9:140497892..140500070,2	K562	blood:
10	chr9:140480405..140490432-chr9:140494944..140502746,26	K562	blood:
11	chr9:140470766..140479486-chr9:140497266..140502997,13	MCF-7	breast:
12	chr9:140470600..140473358-chr9:140498484..140501413,2	K562	blood:
13	chr9:140444986..140448753-chr9:140497892..140501428,4	K562	blood:

No data

Variant related genes	Relation type
ARRDC1	TF binding region
ENSG00000165724	Chromatin interaction
ENSG00000148399	Chromatin interaction
ENSG00000182154	Chromatin interaction
ENSG00000130653	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:39 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894452	chr9:139598108-140523429	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	nsv894499	chr9:139810595-140734161	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
3	nsv531664	chr9:140110329-140725056	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	275 gene(s)	inside rSNPs	diseases
4	nsv531654	chr9:140110329-141033187	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	281 gene(s)	inside rSNPs	diseases
5	nsv1047563	chr9:140219047-140560852	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
6	nsv540357	chr9:140219047-140560852	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
7	nsv531602	chr9:140240417-140535223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	diseases
8	nsv932633	chr9:140240417-141053535	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
9	nsv1035524	chr9:140251014-140751633	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
10	nsv1053628	chr9:140260666-141005637	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
11	nsv534215	chr9:140286134-141008915	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS 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	105 gene(s)	inside rSNPs	n/a
12	nsv1035388	chr9:140306746-140654768	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	n/a
13	nsv831762	chr9:140338779-140514107	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	n/a
14	nsv1039672	chr9:140343466-140707505	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
15	nsv540358	chr9:140343466-140707505	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
16	nsv1041512	chr9:140350404-140612859	Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
17	nsv540359	chr9:140350404-140612859	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
18	nsv616022	chr9:140372570-140523429	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	n/a
19	nsv616023	chr9:140372570-140602887	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
20	nsv531603	chr9:140378700-140590977	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
21	nsv531665	chr9:140378700-141073897	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	n/a
22	nsv868924	chr9:140407572-141053525	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	n/a
23	nsv1039933	chr9:140408112-141005637	Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
24	nsv531666	chr9:140409395-141015925	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS 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	68 gene(s)	inside rSNPs	n/a
25	nsv616024	chr9:140414410-140536098	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	n/a
26	nsv831763	chr9:140439831-140614021	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	n/a
27	nsv540364	chr9:140447860-140514807	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	n/a
28	esv3398333	chr9:140451462-140814795	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers 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	60 gene(s)	inside rSNPs	n/a
29	nsv1052036	chr9:140452641-141018985	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
30	nsv540365	chr9:140452641-141018985	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
31	nsv949702	chr9:140466816-141027939	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Flanking 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	62 gene(s)	inside rSNPs	n/a
32	nsv531667	chr9:140468821-140936261	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
33	nsv894665	chr9:140469600-140523429	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	n/a
34	nsv894666	chr9:140470564-140518576	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	n/a
35	nsv894667	chr9:140473729-140518576	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	n/a
36	nsv894668	chr9:140477812-140518576	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	n/a
37	nsv531668	chr9:140492807-140986221	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	n/a
38	esv3372704	chr9:140498156-140501504	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a
39	esv3378384	chr9:140498481-140501329	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140485800-140499000	Weak transcription	Right Atrium	heart
2	chr9:140485800-140499000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:140493400-140498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:140493400-140499000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:140493400-140499000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:140493400-140499000	Weak transcription	Gastric	stomach
7	chr9:140493600-140499000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:140496400-140498800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr9:140496400-140498800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:140496400-140499400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr9:140496600-140499000	Enhancers	K562	blood
12	chr9:140497000-140498800	Enhancers	Primary hematopoietic stem cells	blood
13	chr9:140497000-140499000	Enhancers	Brain Anterior Caudate	brain
14	chr9:140497400-140498800	Weak transcription	A549	lung
15	chr9:140497400-140499000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr9:140497400-140499400	Enhancers	Spleen	Spleen
17	chr9:140497600-140499000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr9:140497600-140499600	Weak transcription	Brain Substantia Nigra	brain
19	chr9:140497600-140500200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:140497800-140498800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr9:140497800-140498800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:140497800-140498800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:140497800-140498800	Enhancers	Brain Angular Gyrus	brain
24	chr9:140497800-140499000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr9:140498000-140498800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:140498000-140499000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:140498000-140499000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr9:140498000-140499600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr9:140498000-140500000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:140498400-140498800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:140498400-140498800	Enhancers	Esophagus	oesophagus
32	chr9:140498400-140498800	Bivalent Enhancer	NHLF	lung
33	chr9:140498400-140499000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr9:140498400-140499000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr9:140498400-140499000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr9:140498400-140499000	Enhancers	HMEC	breast
37	chr9:140498400-140499200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr9:140498400-140499200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:140498400-140499200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:140498400-140499200	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr9:140498400-140499400	Enhancers	Placenta	Placenta
42	chr9:140498400-140499600	Enhancers	Fetal Lung	lung
43	chr9:140498600-140498800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
44	chr9:140498600-140498800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
45	chr9:140498600-140498800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr9:140498600-140498800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:140498600-140498800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr9:140498600-140498800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
49	chr9:140498600-140498800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr9:140498600-140498800	Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links