Variant report

Variant	rs540253691
Chromosome Location	chr2:20550610-20550611
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	chr2:20549851-20551204	ECC-1	luminal epithelium:	n/a	n/a
2	HDAC2	chr2:20549866-20551770	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:20549865-20551502	Hela-S3	cervix:	n/a	n/a
4	ELF1	chr2:20550514-20550910	A549	lung:	n/a	n/a
5	ELF1	chr2:20549789-20551431	GM12878	blood:	n/a	chr2:20550275-20550287 chr2:20550093-20550105
6	POLR2A	chr2:20549768-20551450	K562	blood:	n/a	n/a
7	YY1	chr2:20550398-20550998	GM12891	blood:	n/a	chr2:20550583-20550597 chr2:20550606-20550615 chr2:20550562-20550584 chr2:20550599-20550610 chr2:20550573-20550581 chr2:20550580-20550594
8	MAX	chr2:20549178-20551690	NB4	blood:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20549687-20549694 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618
9	E2F6	chr2:20550420-20551315	H1-hESC	embryonic stem cell:	n/a	chr2:20551300-20551314 chr2:20550994-20551003 chr2:20550858-20550867 chr2:20550738-20550747
10	POLR2A	chr2:20549757-20551688	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:20549882-20551507	GM15510	blood:	n/a	n/a
12	NFIC	chr2:20549819-20551919	HepG2	liver:	n/a	n/a
13	PML	chr2:20549570-20552013	GM12878	blood:	n/a	n/a
14	CTCF	chr2:20550580-20550730	GM12875	blood:	n/a	n/a
15	MYC	chr2:20549876-20551253	K562	blood:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618
16	MAX	chr2:20549773-20551571	HCT-116	colon:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618
17	MXI1	chr2:20550573-20551327	K562	blood:	n/a	n/a
18	MAX	chr2:20549845-20551694	HepG2	liver:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618
19	BHLHE40	chr2:20550012-20551708	HepG2	liver:	n/a	chr2:20550359-20550375
20	EP300	chr2:20550453-20550885	SK-N-SH_RA	brain:	n/a	chr2:20550830-20550846
21	EGR1	chr2:20549869-20551227	K562	blood:	n/a	chr2:20550609-20550619 chr2:20550738-20550747 chr2:20550990-20550999
22	MYC	chr2:20548541-20551934	A549	lung:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20549687-20549694 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618
23	TAF1	chr2:20550478-20551357	GM12878	blood:	n/a	n/a
24	ZBTB7A	chr2:20550532-20551141	K562	blood:	n/a	n/a
25	TAF1	chr2:20550496-20551165	K562	blood:	n/a	n/a
26	POLR2A	chr2:20550160-20551406	GM12878	blood:	n/a	n/a
27	FOSL1	chr2:20550595-20550921	H1-hESC	embryonic stem cell:	n/a	chr2:20550606-20550615
28	TAF1	chr2:20550507-20551499	H1-neurons	neurons:	n/a	n/a
29	USF1	chr2:20550516-20550943	SK-N-SH_RA	brain:	n/a	n/a
30	POLR2A	chr2:20549968-20551333	MCF-7	breast:	n/a	n/a
31	MYC	chr2:20549298-20551497	K562	blood:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20549687-20549694 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618
32	MAX	chr2:20549967-20551156	HUVEC	blood vessel:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618
33	TAF1	chr2:20549873-20551586	HepG2	liver:	n/a	n/a
34	SP1	chr2:20549831-20551646	A549	lung:	n/a	chr2:20550180-20550192 chr2:20550647-20550656 chr2:20550795-20550809 chr2:20550180-20550192 chr2:20550796-20550805 chr2:20550085-20550095 chr2:20550599-20550611 chr2:20550607-20550619 chr2:20550608-20550618 chr2:20550182-20550191 chr2:20550607-20550619 chr2:20550609-20550618 chr2:20550600-20550614 chr2:20550181-20550191 chr2:20550601-20550610 chr2:20550608-20550617 chr2:20550181-20550195
35	SIN3AK20	chr2:20550483-20550924	PFSK-1	brain:	n/a	n/a
36	CTCF	chr2:20550600-20550750	HCM	heart:	n/a	n/a
37	TCF12	chr2:20549868-20551170	ECC-1	luminal epithelium:	n/a	n/a
38	RUNX3	chr2:20549671-20551704	GM12878	blood:	n/a	n/a
39	POLR2A	chr2:20549573-20551489	K562	blood:	n/a	n/a
40	TBP	chr2:20550557-20551368	Hela-S3	cervix:	n/a	n/a
41	USF1	chr2:20550501-20551017	K562	blood:	n/a	n/a
42	MTA3	chr2:20549639-20551928	GM12878	blood:	n/a	n/a
43	MYC	chr2:20549983-20551293	MCF-7	breast:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618
44	POLR2A	chr2:20550495-20551053	HepG2	liver:	n/a	n/a
45	MAX	chr2:20549759-20551639	GM12878	blood:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618
46	SIN3A	chr2:20549325-20551540	H1-hESC	embryonic stem cell:	n/a	chr2:20550248-20550259 chr2:20551488-20551497 chr2:20551487-20551495
47	USF1	chr2:20550506-20551042	A549	lung:	n/a	n/a
48	TBP	chr2:20549961-20551521	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr2:20549582-20551534	GM12892	blood:	n/a	n/a
50	MAZ	chr2:20549395-20551866	IMR90	lung:	n/a	chr2:20550901-20550910 chr2:20550763-20550772 chr2:20549687-20549694 chr2:20550764-20550771 chr2:20550761-20550772 chr2:20550795-20550805 chr2:20550083-20550092 chr2:20550608-20550618

No.	Distal block	Cell Line	Cell type
1	chr2:20525204..20529381-chr2:20546645..20551782,7	K562	blood:
2	chr2:20099437..20102980-chr2:20547960..20551663,4	K562	blood:
3	chr12:48572524..48575406-chr2:20550361..20552479,2	MCF-7	breast:
4	chr2:20550212..20550981-chr6:144416243..144417147,2	NB4	blood:
5	chr1:52194828..52195735-chr2:20549887..20550726,2	Hela-S3	cervix:
6	chr2:20549379..20553875-chr2:20644345..20648832,13	MCF-7	breast:
7	chr2:20523318..20529381-chr2:20544822..20552572,11	K562	blood:
8	chr2:20548847..20552407-chr2:20645405..20649585,5	MCF-7	breast:
9	chr2:20549000..20550935-chr2:20649579..20652329,2	MCF-7	breast:
10	chr2:20549505..20552081-chr2:20849266..20851365,2	MCF-7	breast:

Variant related genes	Relation type
PUM2	TF binding region
ENSG00000169976	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000271991	Chromatin interaction
ENSG00000117859	Chromatin interaction

Extended variants
information (count: 1 )
Associated
traits (count: 0)

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3423314	chr2:20549496-20552044	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20547600-20551800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:20547800-20551400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:20548200-20550800	Active TSS	Stomach Smooth Muscle	stomach
4	chr2:20548400-20551000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr2:20548400-20551000	Active TSS	Colonic Mucosa	Colon
6	chr2:20548400-20551000	Active TSS	Fetal Intestine Large	intestine
7	chr2:20548400-20551200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:20548400-20551600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:20548600-20550800	Active TSS	Placenta	Placenta
10	chr2:20548600-20551000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr2:20548600-20551000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr2:20548600-20551000	Active TSS	A549	lung
13	chr2:20548600-20551000	Active TSS	K562	blood
14	chr2:20548600-20551200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr2:20548600-20551200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr2:20548600-20551200	Active TSS	Fetal Intestine Small	intestine
17	chr2:20548600-20551200	Active TSS	Fetal Thymus	thymus
18	chr2:20548600-20551400	Active TSS	Right Ventricle	heart
19	chr2:20548600-20551600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:20548600-20551600	Active TSS	Ovary	ovary
21	chr2:20548600-20551800	Active TSS	Thymus	Thymus
22	chr2:20548800-20550800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:20548800-20551000	Active TSS	Primary T cells fromperipheralblood	blood
24	chr2:20548800-20551000	Active TSS	Fetal Brain Female	brain
25	chr2:20548800-20551000	Active TSS	Fetal Muscle Leg	muscle
26	chr2:20548800-20551000	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr2:20548800-20551200	Active TSS	Fetal Lung	lung
28	chr2:20548800-20551200	Active TSS	NHDF-Ad	bronchial
29	chr2:20548800-20551400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:20548800-20551400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:20548800-20551600	Active TSS	Fetal Kidney	kidney
32	chr2:20548800-20551600	Active TSS	Psoas Muscle	Psoas
33	chr2:20549000-20550800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr2:20549000-20550800	Active TSS	Fetal Brain Male	brain
35	chr2:20549000-20550800	Active TSS	HMEC	breast
36	chr2:20549000-20550800	Active TSS	NH-A	brain
37	chr2:20549000-20551000	Active TSS	GM12878-XiMat	blood
38	chr2:20549000-20551000	Active TSS	HSMMtube	muscle
39	chr2:20549000-20551200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:20549000-20551200	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr2:20549000-20551200	Active TSS	Brain Hippocampus Middle	brain
42	chr2:20549000-20551200	Active TSS	Hela-S3	cervix
43	chr2:20549000-20551200	Active TSS	NHLF	lung
44	chr2:20549000-20552000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:20549200-20550800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:20549200-20550800	Active TSS	Fetal Muscle Trunk	muscle
47	chr2:20549200-20551000	Active TSS	Fetal Stomach	stomach
48	chr2:20549200-20551000	Active TSS	HSMM	muscle
49	chr2:20549200-20551000	Active TSS	NHEK	skin
50	chr2:20549200-20551200	Active TSS	HUES64 Cell Line	embryonic stem cell

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