Variant report

Variant	rs3758246
Chromosome Location	chr9:100615122-100615123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr9:100615056-100615239	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTBP2	chr9:100613864-100616060	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr9:100614820-100615239	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr9:100613856-100618340	H1-hESC	embryonic stem cell:	n/a	n/a
5	SUZ12	chr9:100612750-100618219	NT2-D1	testis:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:100615084-100615134	K562	blood:	n/a
2	chr9:100615084-100615134	HCF	heart:	n/a
3	chr9:100615084-100615134	HIPEpiC	eye:	n/a
4	chr9:100615084-100615134	GM06990	blood:	n/a
5	chr9:100615084-100615134	MCF-7	breast:	n/a
6	chr9:100615084-100615134	IMR90	lung:	fetal
7	chr9:100615084-100615134	HRCEpiC	kidney:	n/a
8	chr9:100615084-100615134	Jurkat	blood:	n/a
9	chr9:100615084-100615134	Hela-S3	cervix:	n/a
10	chr9:100615084-100615134	NHBE	bronchial:	n/a
11	chr9:100615084-100615134	HEEpiC	esophagus:	n/a
12	chr9:100615084-100615134	ovcar-3	ovarian:	n/a
13	chr9:100615084-100615134	NH-A	brain:	n/a
14	chr9:100615084-100615134	NT2-D1	testis:	n/a
15	chr9:100615084-100615134	AG04450	lung:	fetal
16	chr9:100615084-100615134	AG09319	gingival:	n/a
17	chr9:100615084-100615134	BJ	skin:	n/a
18	chr9:100615084-100615134	HMEC	breast:	n/a
19	chr9:100615084-100615134	Hepatocyte	liver:	n/a
20	chr9:100615084-100615134	NHDF-neo	bronchial:	n/a
21	chr9:100615084-100615134	HAEpiC	amniotic membrane:	n/a
22	chr9:100615084-100615134	AoSMC	blood vessel:	n/a
23	chr9:100615084-100615134	HCM	heart:	n/a
24	chr9:100615084-100615134	U87	brain:	n/a
25	chr9:100615084-100615134	MCF10A-Er-Src	breast:	n/a
26	chr9:100615084-100615134	RPTEC	kidney:	n/a
27	chr9:100615084-100615134	SK-N-SH_RA	brain:	n/a
28	chr9:100615084-100615134	HCPEpiC	choroid plexus:	n/a
29	chr9:100615084-100615134	GM19239	blood:	n/a
30	chr9:100615084-100615134	AG04449	skin:	fetal
31	chr9:100615084-100615134	LNCaP	prostate:	n/a
32	chr9:100615084-100615134	A549	lung:	n/a
33	chr9:100615084-100615134	HEK293	kidney:	embryo
34	chr9:100615084-100615134	GM12878	blood:	n/a
35	chr9:100615084-100615134	NB4	blood:	n/a
36	chr9:100615084-100615134	SK-N-MC	brain:	n/a
37	chr9:100615084-100615134	HRPEpiC	eye:	n/a
38	chr9:100615084-100615134	PrEC	prostate:	n/a
39	chr9:100615084-100615134	HRE	kidney:	n/a
40	chr9:100615084-100615134	SK-N-SH	brain:	n/a
41	chr9:100615084-100615134	AG10803	skin:	n/a
42	chr9:100615084-100615134	HNPCEpiC	eye:	n/a
43	chr9:100615084-100615134	T-47D	breast:	n/a
44	chr9:100615084-100615134	H1-hESC	embryonic stem cell:	embryo
45	chr9:100615084-100615134	SAEC	small airway:	n/a
46	chr9:100615084-100615134	HCT-116	colon:	n/a
47	chr9:100615084-100615134	BE2_C	brain:	n/a
48	chr9:100615084-100615134	HPAEpiC	pulmonary alveolar:	n/a
49	chr9:100615084-100615134	HL-60	blood:	n/a
50	chr9:100615084-100615134	AG09309	skin:	n/a

No data

Variant related genes	Relation type
FOXE1	TF binding region
FOXE1	CpG island

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs57898891	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv825000	chr9:100613121-100618319	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3330300	chr9:100613506-100618154	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3421459	chr9:100614656-100617704	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100613400-100615400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:100613400-100615600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr9:100613400-100615600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
4	chr9:100613400-100615600	Bivalent Enhancer	Spleen	Spleen
5	chr9:100613400-100618800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:100613600-100615200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
7	chr9:100613600-100618000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr9:100613800-100615200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr9:100613800-100615400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
10	chr9:100613800-100615600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr9:100613800-100615600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
12	chr9:100613800-100615800	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr9:100613800-100616200	Bivalent Enhancer	Liver	Liver
14	chr9:100613800-100616400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:100613800-100616400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr9:100613800-100616400	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr9:100613800-100616400	Bivalent Enhancer	Fetal Stomach	stomach
18	chr9:100613800-100616600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr9:100613800-100616800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr9:100613800-100617400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
21	chr9:100613800-100617800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr9:100614000-100615400	Enhancers	Pancreas	Pancrea
23	chr9:100614000-100615600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:100614000-100615600	Bivalent Enhancer	Adipose Nuclei	Adipose
25	chr9:100614000-100615600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
26	chr9:100614000-100615800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:100614000-100616400	Bivalent Enhancer	Lung	lung
28	chr9:100614000-100616600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
29	chr9:100614000-100617800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
30	chr9:100614000-100617800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:100614200-100615400	Weak transcription	Gastric	stomach
32	chr9:100614200-100615600	Bivalent/Poised TSS	Esophagus	oesophagus
33	chr9:100614400-100615200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
34	chr9:100614400-100616400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr9:100614400-100616400	Bivalent Enhancer	Fetal Intestine Small	intestine
36	chr9:100614600-100615200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:100614600-100615200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:100614600-100615200	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
39	chr9:100614600-100615200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
40	chr9:100614600-100615600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr9:100614600-100615600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:100614600-100615600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
43	chr9:100614600-100616400	Bivalent Enhancer	Fetal Brain Male	brain
44	chr9:100614600-100616400	Bivalent Enhancer	Left Ventricle	heart
45	chr9:100614600-100616600	Bivalent Enhancer	Placenta	Placenta
46	chr9:100614800-100615200	Bivalent Enhancer	Brain Angular Gyrus	brain
47	chr9:100614800-100615200	Bivalent Enhancer	Brain Germinal Matrix	brain
48	chr9:100614800-100615200	Bivalent Enhancer	Colon Smooth Muscle	Colon
49	chr9:100614800-100615200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
50	chr9:100614800-100615400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain

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