Variant report

Variant	rs201865532
Chromosome Location	chr9:21318629-21318630
allele	-/AC
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	REST	chr9:21318161-21319042	H1-neurons	neurons:	n/a	n/a
2	CTCF	chr9:21318480-21318630	WI-38	lung:	n/a	n/a
3	CTCF	chr9:21318226-21318893	HCT-116	colon:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
4	CTCF	chr9:21318187-21318716	MCF-7	breast:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
5	SMC3	chr9:21318256-21318875	GM12878	blood:	n/a	chr9:21318470-21318484 chr9:21318607-21318615
6	CTCF	chr9:21318219-21318671	IMR90	lung:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
7	RAD21	chr9:21318200-21318840	HCT-116	colon:	n/a	chr9:21318469-21318488
8	RAD21	chr9:21318318-21318706	SK-N-SH_RA	brain:	n/a	chr9:21318469-21318488
9	CTCF	chr9:21318330-21318647	T-47D	breast:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
10	CTCF	chr9:21318480-21318630	HFF-Myc	foreskin:	n/a	n/a
11	SMC3	chr9:21318328-21318643	HepG2	liver:	n/a	chr9:21318470-21318484 chr9:21318607-21318615
12	RAD21	chr9:21318312-21318682	HepG2	liver:	n/a	chr9:21318469-21318488
13	RAD21	chr9:21318332-21318645	GM12878	blood:	n/a	chr9:21318469-21318488
14	CTCF	chr9:21318325-21318633	A549	lung:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
15	CTCF	chr9:21318343-21318717	A549	lung:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
16	RAD21	chr9:21318292-21318679	Hela-S3	cervix:	n/a	chr9:21318469-21318488
17	MAX	chr9:21318003-21318660	NB4	blood:	n/a	n/a
18	SMC3	chr9:21318168-21319039	SK-N-SH	brain:	n/a	chr9:21318470-21318484 chr9:21318607-21318615
19	RAD21	chr9:21318230-21318701	A549	lung:	n/a	chr9:21318469-21318488
20	CTCF	chr9:21318250-21318702	GM12878	blood:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
21	REST	chr9:21318359-21319027	H1-neurons	neurons:	n/a	n/a
22	RAD21	chr9:21318217-21318774	A549	lung:	n/a	chr9:21318469-21318488
23	RFX5	chr9:21318620-21318663	H1-hESC	embryonic stem cell:	n/a	n/a
24	RFX5	chr9:21318228-21319070	SK-N-SH	brain:	n/a	n/a
25	ZNF143	chr9:21318292-21318668	GM12878	blood:	n/a	n/a
26	RAD21	chr9:21318307-21318732	MCF-7	breast:	n/a	chr9:21318469-21318488
27	RAD21	chr9:21318253-21318781	MCF-7	breast:	n/a	chr9:21318469-21318488
28	CTCF	chr9:21318135-21319004	A549	lung:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
29	RAD21	chr9:21318297-21318678	H1-hESC	embryonic stem cell:	n/a	chr9:21318469-21318488
30	TBL1XR1	chr9:21318419-21318644	GM12878	blood:	n/a	n/a
31	SMC3	chr9:21318284-21318702	Hela-S3	cervix:	n/a	chr9:21318470-21318484 chr9:21318607-21318615
32	TBP	chr9:21318508-21318745	GM12878	blood:	n/a	n/a
33	CTCF	chr9:21318335-21318676	A549	lung:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
34	CTCF	chr9:21318480-21318630	HCM	heart:	n/a	n/a
35	CTCF	chr9:21318331-21318656	A549	lung:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
36	CTCF	chr9:21318215-21318704	HepG2	liver:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
37	RAD21	chr9:21318287-21318722	GM12878	blood:	n/a	chr9:21318469-21318488
38	RAD21	chr9:21318364-21318763	ECC-1	luminal epithelium:	n/a	chr9:21318469-21318488
39	RAD21	chr9:21318306-21318658	IMR90	lung:	n/a	chr9:21318469-21318488
40	RAD21	chr9:21318272-21318728	HepG2	liver:	n/a	chr9:21318469-21318488
41	CTCF	chr9:21318383-21318750	MCF-7	breast:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
42	RAD21	chr9:21317967-21318892	SK-N-SH	brain:	n/a	chr9:21318469-21318488
43	MYC	chr9:21318239-21318973	NB4	blood:	n/a	n/a
44	RAD21	chr9:21318215-21318670	H1-hESC	embryonic stem cell:	n/a	chr9:21318469-21318488
45	RAD21	chr9:21318316-21318732	ECC-1	luminal epithelium:	n/a	chr9:21318469-21318488
46	CTCF	chr9:21318620-21318770	A549	lung:	n/a	n/a
47	RAD21	chr9:21318207-21318734	HCT-116	colon:	n/a	chr9:21318469-21318488
48	CTCF	chr9:21317947-21318977	SK-N-SH	brain:	n/a	chr9:21318469-21318485 chr9:21318468-21318486 chr9:21318470-21318491 chr9:21318471-21318484
49	RAD21	chr9:21318282-21318807	SK-N-SH_RA	brain:	n/a	chr9:21318469-21318488
50	RAD21	chr9:21318339-21318720	H1-hESC	embryonic stem cell:	n/a	chr9:21318469-21318488

No.	Distal block	Cell Line	Cell type
1	chr9:21317956..21318799-chr9:21455067..21455992,4	MCF-7	breast:
2	chr9:21318010..21319069-chr9:21395893..21396720,4	MCF-7	breast:
3	chr9:21318068..21318780-chr9:21789413..21789937,2	MCF-7	breast:
4	chr9:21318056..21318697-chrX:104999680..105000200,2	MCF-7	breast:
5	chr9:21253305..21254010-chr9:21318409..21318973,2	MCF-7	breast:
6	chr9:21317987..21318804-chr9:21455380..21456013,2	MCF-7	breast:

Variant related genes	Relation type
IFNA20P	TF binding region
ENSG00000238271	Chromatin interaction
ENSG00000261696	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
2	nsv892734	chr9:21108817-21323089	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv3429264	chr9:21318302-21321050	Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21309800-21322600	Weak transcription	Brain Substantia Nigra	brain
2	chr9:21312200-21322000	Weak transcription	GM12878-XiMat	blood
3	chr9:21315000-21323000	Weak transcription	Thymus	Thymus
4	chr9:21316200-21322800	Weak transcription	Fetal Lung	lung
5	chr9:21316400-21318800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr9:21316400-21319000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr9:21316400-21322800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:21316600-21321200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:21316600-21322600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:21316600-21322600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:21316600-21322800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:21316600-21322800	Weak transcription	Lung	lung
13	chr9:21316600-21323000	Weak transcription	Pancreas	Pancrea
14	chr9:21316600-21330600	Weak transcription	Small Intestine	intestine
15	chr9:21316800-21319000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:21316800-21322800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:21317000-21320400	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:21317000-21321200	Weak transcription	Primary B cells from cord blood	blood
19	chr9:21317000-21321200	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:21317000-21326800	Weak transcription	Hela-S3	cervix
21	chr9:21317200-21320600	Weak transcription	Liver	Liver
22	chr9:21317200-21322800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr9:21317200-21323000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:21317200-21323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:21317200-21331600	Weak transcription	Esophagus	oesophagus
26	chr9:21317200-21331600	Weak transcription	Gastric	stomach
27	chr9:21317400-21321400	Weak transcription	Osteobl	bone
28	chr9:21317400-21323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:21317600-21321600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr9:21317800-21319000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:21317800-21319000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:21318000-21318800	Enhancers	Brain Cingulate Gyrus	brain
33	chr9:21318000-21318800	Enhancers	NHEK	skin
34	chr9:21318000-21319000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:21318200-21318800	Weak transcription	Fetal Muscle Leg	muscle
36	chr9:21318200-21321200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:21318200-21330000	Weak transcription	Brain Anterior Caudate	brain
38	chr9:21318200-21330400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:21318400-21319000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr9:21318400-21320000	Weak transcription	Primary T cells from cord blood	blood
41	chr9:21318600-21318800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr9:21318600-21318800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr9:21318600-21318800	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr9:21318600-21318800	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr9:21318600-21318800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:21318600-21318800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:21318600-21318800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:21318600-21318800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr9:21318600-21318800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr9:21318600-21318800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links