Variant report

Variant	rs540816010
Chromosome Location	chr9:101569796-101569797
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:90)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:90 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr9:101569704-101570054	K562	blood:	n/a	n/a
2	MAX	chr9:101569783-101570126	K562	blood:	n/a	n/a
3	EGR1	chr9:101569719-101570074	K562	blood:	n/a	chr9:101569928-101569942
4	ELF1	chr9:101569713-101570130	GM12878	blood:	n/a	n/a
5	CTCF	chr9:101568510-101570694	A549	lung:	n/a	chr9:101568822-101568843 chr9:101568820-101568838
6	TAF1	chr9:101569721-101570150	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr9:101569759-101570303	MCF-7	breast:	n/a	n/a
8	MYC	chr9:101569369-101570400	K562	blood:	n/a	n/a
9	SIN3A	chr9:101569521-101570281	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAZ	chr9:101569471-101570119	K562	blood:	n/a	n/a
11	POLR2A	chr9:101569753-101570141	A549	lung:	n/a	n/a
12	POLR2A	chr9:101569647-101570208	HCT-116	colon:	n/a	n/a
13	NR2F2	chr9:101569198-101569926	K562	blood:	n/a	n/a
14	ELF1	chr9:101569511-101570148	HCT-116	colon:	n/a	n/a
15	POLR2A	chr9:101569759-101570194	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr9:101569788-101570092	GM12878	blood:	n/a	n/a
17	JUND	chr9:101569407-101569815	T-47D	breast:	n/a	n/a
18	MAX	chr9:101569742-101570126	A549	lung:	n/a	n/a
19	POLR2A	chr9:101569647-101570144	K562	blood:	n/a	n/a
20	POLR2A	chr9:101569672-101570512	H1-neurons	neurons:	n/a	n/a
21	MAX	chr9:101569742-101570509	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr9:101569643-101570119	U87	brain:	n/a	n/a
23	POLR2A	chr9:101569746-101570376	MCF-7	breast:	n/a	n/a
24	E2F6	chr9:101569085-101570359	K562	blood:	n/a	chr9:101569821-101569831
25	POLR2A	chr9:101569651-101570189	K562	blood:	n/a	n/a
26	POLR2A	chr9:101569669-101570544	K562	blood:	n/a	n/a
27	TAF1	chr9:101569670-101570104	H1-hESC	embryonic stem cell:	n/a	n/a
28	BHLHE40	chr9:101569104-101569848	K562	blood:	n/a	n/a
29	POLR2A	chr9:101569656-101570113	K562	blood:	n/a	n/a
30	POLR2A	chr9:101569792-101570180	GM18951	blood:	n/a	n/a
31	POLR2A	chr9:101569753-101570359	K562	blood:	n/a	n/a
32	ZBTB7A	chr9:101569675-101570252	K562	blood:	n/a	n/a
33	MYC	chr9:101569685-101569883	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr9:101569679-101570357	GM15510	blood:	n/a	n/a
35	POLR2A	chr9:101569689-101570316	A549	lung:	n/a	n/a
36	TAF1	chr9:101569713-101570118	K562	blood:	n/a	n/a
37	POLR2A	chr9:101569703-101570312	H1-hESC	embryonic stem cell:	n/a	n/a
38	GATA3	chr9:101569190-101570151	MCF-7	breast:	n/a	n/a
39	POLR2A	chr9:101569649-101571426	K562	blood:	n/a	n/a
40	SIN3AK20	chr9:101569748-101570129	K562	blood:	n/a	n/a
41	POLR2A	chr9:101569727-101570102	GM12878	blood:	n/a	n/a
42	CCNT2	chr9:101569411-101570498	K562	blood:	n/a	n/a
43	MAX	chr9:101569097-101570259	K562	blood:	n/a	n/a
44	POLR2A	chr9:101569445-101570368	Raji	blood:	n/a	n/a
45	SIN3AK20	chr9:101569301-101569986	MCF-7	breast:	n/a	n/a
46	MAX	chr9:101569102-101570463	K562	blood:	n/a	n/a
47	CBX3	chr9:101569209-101569863	K562	blood:	n/a	n/a
48	TBP	chr9:101569656-101570163	K562	blood:	n/a	n/a
49	MAX	chr9:101569777-101570488	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr9:101569660-101569810	GM12873	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:101568546..101571235-chr9:101609367..101611059,3	MCF-7	breast:
2	chr20:62284408..62284944-chr9:101569753..101570305,2	HCT-116	colon:
3	chr9:101568879..101571340-chr9:101705382..101708339,2	K562	blood:
4	chr9:101556573..101560424-chr9:101566029..101574080,12	MCF-7	breast:
5	chr9:101569010..101571000-chr9:101705834..101707895,2	MCF-7	breast:
6	chr9:101550194..101555244-chr9:101566657..101571786,8	MCF-7	breast:
7	chr9:101551293..101553847-chr9:101568036..101571328,4	K562	blood:
8	chr9:101555483..101562112-chr9:101568669..101573087,9	K562	blood:
9	chr9:101557242..101560519-chr9:101566443..101572716,8	MCF-7	breast:
10	chr9:101552233..101554875-chr9:101569362..101571456,2	K562	blood:
11	chr9:101550225..101553756-chr9:101569289..101571539,3	MCF-7	breast:

No data

Variant related genes	Relation type
GALNT12	TF binding region
ENSG00000270412	Chromatin interaction
ENSG00000204291	Chromatin interaction
ENSG00000165138	Chromatin interaction
ENSG00000119514	Chromatin interaction
ENSG00000197457	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	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv3410897	chr9:101569181-101571179	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101567600-101570000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:101567800-101569800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:101567800-101569800	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr9:101568200-101569800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
5	chr9:101568400-101570600	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr9:101568800-101569800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr9:101569000-101569800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:101569000-101570400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr9:101569200-101569800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:101569200-101569800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr9:101569200-101569800	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr9:101569200-101569800	Flanking Active TSS	Colonic Mucosa	Colon
13	chr9:101569200-101569800	Bivalent/Poised TSS	NH-A	brain
14	chr9:101569200-101570200	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr9:101569200-101570400	Active TSS	Fetal Brain Female	brain
16	chr9:101569200-101571200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr9:101569400-101569800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr9:101569400-101569800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:101569400-101569800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
20	chr9:101569400-101569800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr9:101569400-101569800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr9:101569400-101569800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr9:101569400-101569800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr9:101569400-101569800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr9:101569400-101569800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:101569400-101569800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:101569400-101569800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:101569400-101569800	Enhancers	Aorta	Aorta
29	chr9:101569400-101569800	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr9:101569400-101569800	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr9:101569400-101569800	Flanking Active TSS	Esophagus	oesophagus
32	chr9:101569400-101569800	Flanking Active TSS	Fetal Intestine Large	intestine
33	chr9:101569400-101569800	Flanking Active TSS	Fetal Intestine Small	intestine
34	chr9:101569400-101569800	Active TSS	Fetal Kidney	kidney
35	chr9:101569400-101569800	Flanking Active TSS	Fetal Lung	lung
36	chr9:101569400-101569800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
37	chr9:101569400-101569800	Flanking Active TSS	Fetal Stomach	stomach
38	chr9:101569400-101569800	Enhancers	Placenta Amnion	Placenta Amnion
39	chr9:101569400-101569800	Flanking Active TSS	K562	blood
40	chr9:101569400-101570200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:101569400-101570200	Active TSS	Primary B cells from cord blood	blood
42	chr9:101569400-101570200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr9:101569400-101570200	Active TSS	Fetal Heart	heart
44	chr9:101569400-101570400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:101569400-101570400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:101569400-101571000	Active TSS	H9 Cell Line	embryonic stem cell
47	chr9:101569400-101571000	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr9:101569600-101569800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
49	chr9:101569600-101569800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
50	chr9:101569600-101569800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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