Variant report

Variant	rs552853528
Chromosome Location	chr20:23617845-23617846
allele	A/C
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	chr20:23617614-23618865	HUVEC	blood vessel:	n/a	n/a
2	NR3C1	chr20:23617748-23618203	A549	lung:	n/a	chr20:23617961-23617982 chr20:23617963-23617979 chr20:23617964-23617978
3	POLR2A	chr20:23617842-23618715	Hela-S3	cervix:	n/a	n/a
4	CBX3	chr20:23617792-23618151	K562	blood:	n/a	n/a
5	CTCF	chr20:23617840-23617990	HRE	kidney:	n/a	n/a
6	SIN3AK20	chr20:23617724-23618913	MCF-7	breast:	n/a	n/a
7	POLR2A	chr20:23617840-23618804	A549	lung:	n/a	n/a
8	POLR2A	chr20:23614494-23618787	HepG2	liver:	n/a	n/a
9	MAX	chr20:23617801-23618892	MCF-7	breast:	n/a	n/a
10	MAX	chr20:23617646-23618929	A549	lung:	n/a	n/a
11	ELF1	chr20:23617824-23618891	GM12878	blood:	n/a	chr20:23618216-23618228
12	POLR2A	chr20:23611829-23619325	HepG2	liver:	n/a	n/a
13	POLR2A	chr20:23617828-23618698	Hela-S3	cervix:	n/a	n/a
14	MYBL2	chr20:23617743-23618773	HepG2	liver:	n/a	n/a
15	EGR1	chr20:23617767-23618169	K562	blood:	n/a	chr20:23617977-23617990
16	MXI1	chr20:23617541-23618906	IMR90	lung:	n/a	n/a
17	MAX	chr20:23617840-23618814	MCF-7	breast:	n/a	n/a
18	EGR1	chr20:23617831-23618112	K562	blood:	n/a	chr20:23617977-23617990
19	RCOR1	chr20:23617443-23618713	HepG2	liver:	n/a	n/a
20	ZBTB7A	chr20:23617839-23618412	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr20:23617842-23618822	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr20:23617810-23618757	K562	blood:	n/a	n/a
23	SIN3A	chr20:23617797-23618744	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr20:23617817-23618787	HepG2	liver:	n/a	n/a
25	POLR2A	chr20:23617835-23618705	K562	blood:	n/a	n/a
26	POLR2A	chr20:23617817-23618984	HUVEC	blood vessel:	n/a	n/a
27	SMC3	chr20:23617763-23618089	Hela-S3	cervix:	n/a	n/a
28	REST	chr20:23617750-23618835	H1-neurons	neurons:	n/a	chr20:23618171-23618189
29	HEY1	chr20:23617817-23618852	HepG2	liver:	n/a	chr20:23617977-23617992 chr20:23618207-23618222 chr20:23617985-23618000
30	POLR2A	chr20:23617648-23618776	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr20:23617790-23618808	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr20:23617843-23618905	K562	blood:	n/a	n/a
33	POLR2A	chr20:23616908-23618741	HepG2	liver:	n/a	n/a
34	MYC	chr20:23617831-23618767	K562	blood:	n/a	n/a
35	MBD4	chr20:23616820-23618095	HepG2	liver:	n/a	n/a
36	CREB1	chr20:23617837-23618352	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr20:23617844-23618799	GM18951	blood:	n/a	n/a
38	POLR2A	chr20:23617696-23618752	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr20:23611753-23618814	HepG2	liver:	n/a	n/a
40	MYC	chr20:23617565-23618856	A549	lung:	n/a	n/a
41	UBTF	chr20:23617817-23618747	K562	blood:	n/a	n/a
42	CCNT2	chr20:23617735-23618726	K562	blood:	n/a	chr20:23618218-23618227
43	POLR2A	chr20:23617778-23618804	HepG2	liver:	n/a	n/a
44	POLR2A	chr20:23617301-23618776	IMR90	lung:	n/a	n/a
45	POLR2A	chr20:23615326-23618779	MCF10A-Er-Src	breast:	n/a	n/a
46	MAX	chr20:23617844-23618753	NB4	blood:	n/a	n/a
47	NR3C1	chr20:23617777-23618175	A549	lung:	n/a	chr20:23617961-23617982 chr20:23617963-23617979 chr20:23617964-23617978
48	POLR2A	chr20:23617790-23618771	HUVEC	blood vessel:	n/a	n/a
49	GATA2	chr20:23617675-23618609	SH-SY5Y	brain:	n/a	n/a
50	POLR2A	chr20:23617826-23618823	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:23617167..23619413-chr20:62495612..62498216,2	MCF-7	breast:
2	chr20:23340884..23343229-chr20:23616953..23618725,2	K562	blood:
3	chr20:23400787..23402892-chr20:23617355..23620191,2	MCF-7	breast:
4	chr20:23400310..23402508-chr20:23615661..23618868,3	MCF-7	breast:
5	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
6	chr20:23615491..23618366-chr20:23625789..23627708,2	MCF-7	breast:
7	chr20:23342009..23344759-chr20:23616093..23619702,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270001	TF binding region
ENSG00000125814	Chromatin interaction
ENSG00000125812	Chromatin interaction
ENSG00000101150	Chromatin interaction
ENSG00000270001	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers 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	42 gene(s)	inside rSNPs	diseases
2	nsv964381	chr20:23614805-23621846	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	esv3359195	chr20:23617352-23620750	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	esv3377051	chr20:23617777-23620325	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23610400-23618200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:23615000-23618000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
3	chr20:23615800-23618000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr20:23616400-23618600	Active TSS	Brain Hippocampus Middle	brain
5	chr20:23616800-23618000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
6	chr20:23616800-23618600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr20:23617000-23618000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr20:23617000-23618000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
9	chr20:23617000-23618000	Flanking Active TSS	GM12878-XiMat	blood
10	chr20:23617000-23618200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr20:23617000-23618400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr20:23617000-23618600	Active TSS	Brain Substantia Nigra	brain
13	chr20:23617200-23618000	Flanking Active TSS	Fetal Brain Male	brain
14	chr20:23617200-23618000	Flanking Active TSS	Fetal Muscle Leg	muscle
15	chr20:23617200-23618800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr20:23617200-23618800	Active TSS	Brain Cingulate Gyrus	brain
17	chr20:23617400-23618000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr20:23617400-23618000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr20:23617400-23618000	Flanking Active TSS	Fetal Lung	lung
20	chr20:23617400-23618000	Flanking Active TSS	K562	blood
21	chr20:23617400-23618600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr20:23617400-23618600	Active TSS	Brain Angular Gyrus	brain
23	chr20:23617400-23618600	Active TSS	Esophagus	oesophagus
24	chr20:23617400-23618600	Active TSS	Fetal Intestine Small	intestine
25	chr20:23617400-23618600	Active TSS	Left Ventricle	heart
26	chr20:23617400-23618600	Active TSS	Ovary	ovary
27	chr20:23617400-23618600	Active TSS	NHDF-Ad	bronchial
28	chr20:23617400-23618800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr20:23617400-23618800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr20:23617400-23618800	Active TSS	Psoas Muscle	Psoas
31	chr20:23617400-23618800	Active TSS	Right Atrium	heart
32	chr20:23617400-23618800	Active TSS	Right Ventricle	heart
33	chr20:23617600-23618000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
34	chr20:23617600-23618000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr20:23617600-23618000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr20:23617600-23618000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr20:23617600-23618200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr20:23617600-23618400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
39	chr20:23617600-23618600	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr20:23617600-23618600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr20:23617600-23618600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr20:23617600-23618600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr20:23617600-23618600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr20:23617600-23618600	Active TSS	Primary T cells from cord blood	blood
45	chr20:23617600-23618600	Active TSS	Aorta	Aorta
46	chr20:23617600-23618600	Active TSS	Colon Smooth Muscle	Colon
47	chr20:23617600-23618600	Active TSS	Duodenum Mucosa	Duodenum
48	chr20:23617600-23618600	Active TSS	Fetal Kidney	kidney
49	chr20:23617600-23618600	Active TSS	Gastric	stomach
50	chr20:23617600-23618600	Active TSS	Sigmoid Colon	Sigmoid Colon

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