Variant report

Variant	rs539167750
Chromosome Location	chr2:20551042-20551043
allele	A/T
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	FOXA1	chr2:20551035-20551829	HepG2	liver:	n/a	chr2:20551475-20551490
2	POLR2A	chr2:20549851-20551204	ECC-1	luminal epithelium:	n/a	n/a
3	HDAC2	chr2:20549866-20551770	HepG2	liver:	n/a	n/a
4	TAF1	chr2:20551027-20551321	GM12891	blood:	n/a	n/a
5	POLR2A	chr2:20549865-20551502	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:20550612-20551460	GM12891	blood:	n/a	n/a
7	ELF1	chr2:20549789-20551431	GM12878	blood:	n/a	chr2:20550275-20550287 chr2:20550093-20550105
8	POLR2A	chr2:20549768-20551450	K562	blood:	n/a	n/a
9	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
10	E2F6	chr2:20550420-20551315	H1-hESC	embryonic stem cell:	n/a	chr2:20551300-20551314 chr2:20550994-20551003 chr2:20550858-20550867 chr2:20550738-20550747
11	POLR2A	chr2:20549757-20551688	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:20549882-20551507	GM15510	blood:	n/a	n/a
13	NFIC	chr2:20549819-20551919	HepG2	liver:	n/a	n/a
14	PML	chr2:20549570-20552013	GM12878	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	EGR1	chr2:20549869-20551227	K562	blood:	n/a	chr2:20550609-20550619 chr2:20550738-20550747 chr2:20550990-20550999
21	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
22	TAF1	chr2:20550478-20551357	GM12878	blood:	n/a	n/a
23	CHD1	chr2:20550914-20551100	H1-hESC	embryonic stem cell:	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	TAF1	chr2:20550507-20551499	H1-neurons	neurons:	n/a	n/a
28	CTCF	chr2:20551000-20551150	WERI-Rb-1	eye:	n/a	n/a
29	POLR2A	chr2:20549968-20551333	MCF-7	breast:	n/a	n/a
30	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
31	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
32	TAF1	chr2:20549873-20551586	HepG2	liver:	n/a	n/a
33	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
34	TCF3	chr2:20550629-20551346	GM12878	blood:	n/a	chr2:20551184-20551194 chr2:20551179-20551192
35	TCF12	chr2:20549868-20551170	ECC-1	luminal epithelium:	n/a	n/a
36	RUNX3	chr2:20549671-20551704	GM12878	blood:	n/a	n/a
37	POLR2A	chr2:20549573-20551489	K562	blood:	n/a	n/a
38	TBP	chr2:20550557-20551368	Hela-S3	cervix:	n/a	n/a
39	MXI1	chr2:20550629-20551229	H1-hESC	embryonic stem cell:	n/a	n/a
40	MTA3	chr2:20549639-20551928	GM12878	blood:	n/a	n/a
41	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
42	POLR2A	chr2:20550495-20551053	HepG2	liver:	n/a	n/a
43	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
44	SIN3A	chr2:20549325-20551540	H1-hESC	embryonic stem cell:	n/a	chr2:20550248-20550259 chr2:20551488-20551497 chr2:20551487-20551495
45	USF1	chr2:20550506-20551042	A549	lung:	n/a	n/a
46	TBP	chr2:20549961-20551521	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr2:20549582-20551534	GM12892	blood:	n/a	n/a
48	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
49	POLR2A	chr2:20549959-20551291	U87	brain:	n/a	n/a
50	POLR2A	chr2:20549855-20551649	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20550911..20553369-chr2:20646204..20648737,2	K562	blood:
2	chr2:20550750..20552615-chr2:21021758..21023805,2	K562	blood:
3	chr2:20525204..20529381-chr2:20546645..20551782,7	K562	blood:
4	chr2:20099437..20102980-chr2:20547960..20551663,4	K562	blood:
5	chr12:48572524..48575406-chr2:20550361..20552479,2	MCF-7	breast:
6	chr2:20549379..20553875-chr2:20644345..20648832,13	MCF-7	breast:
7	chr2:20526069..20526648-chr2:20550792..20551493,2	K562	blood:
8	chr2:20523318..20529381-chr2:20544822..20552572,11	K562	blood:
9	chr2:20548847..20552407-chr2:20645405..20649585,5	MCF-7	breast:
10	chr2:20549505..20552081-chr2:20849266..20851365,2	MCF-7	breast:

Variant related genes	Relation type
PUM2	TF binding region
ENSG00000183891	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000271991	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000118961	Chromatin interaction
ENSG00000055917	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	chr2:20548400-20551200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:20548400-20551600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr2:20548600-20551200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr2:20548600-20551200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr2:20548600-20551200	Active TSS	Fetal Intestine Small	intestine
8	chr2:20548600-20551200	Active TSS	Fetal Thymus	thymus
9	chr2:20548600-20551400	Active TSS	Right Ventricle	heart
10	chr2:20548600-20551600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:20548600-20551600	Active TSS	Ovary	ovary
12	chr2:20548600-20551800	Active TSS	Thymus	Thymus
13	chr2:20548800-20551200	Active TSS	Fetal Lung	lung
14	chr2:20548800-20551200	Active TSS	NHDF-Ad	bronchial
15	chr2:20548800-20551400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:20548800-20551400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:20548800-20551600	Active TSS	Fetal Kidney	kidney
18	chr2:20548800-20551600	Active TSS	Psoas Muscle	Psoas
19	chr2:20549000-20551200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:20549000-20551200	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr2:20549000-20551200	Active TSS	Brain Hippocampus Middle	brain
22	chr2:20549000-20551200	Active TSS	Hela-S3	cervix
23	chr2:20549000-20551200	Active TSS	NHLF	lung
24	chr2:20549000-20552000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:20549200-20551200	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr2:20549200-20551200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:20549200-20551200	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr2:20549200-20551200	Active TSS	Osteobl	bone
29	chr2:20549200-20551400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr2:20549200-20551400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr2:20549200-20551400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:20549200-20551800	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr2:20549200-20551800	Active TSS	Aorta	Aorta
34	chr2:20549400-20551200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:20549400-20551200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:20549400-20551200	Active TSS	Brain Substantia Nigra	brain
37	chr2:20549400-20551200	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr2:20549400-20551200	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr2:20549400-20551400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:20549400-20551400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr2:20549400-20551400	Active TSS	Brain Angular Gyrus	brain
42	chr2:20549600-20551200	Active TSS	Primary B cells from peripheral blood	blood
43	chr2:20549600-20551200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr2:20549600-20551200	Active TSS	Brain Anterior Caudate	brain
45	chr2:20549600-20551200	Active TSS	Brain Cingulate Gyrus	brain
46	chr2:20549600-20551200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:20549600-20551200	Active TSS	Colon Smooth Muscle	Colon
48	chr2:20549600-20551200	Active TSS	Lung	lung
49	chr2:20549600-20551200	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr2:20549600-20551200	Active TSS	Rectal Smooth Muscle	rectum

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